Contacts of the helix formed by residues 15 - 36 (chain B) in PDB entry 3SDL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY 3.2 1.4 + - - -
14B PRO* 1.3 78.1 - - - +
16B ALA* 1.3 63.0 + - - +
17B THR 3.3 1.1 - - - -
18B ASN* 3.6 9.3 + - - +
19B ALA* 3.3 20.3 + - - +
11D ALA* 4.7 7.3 - - - +
13D ASN* 6.3 2.9 - - - -
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ARG 4.6 0.2 - - - +
39A ALA* 3.1 25.4 - - - +
41A ASP* 3.8 12.1 - - + +
12B VAL* 3.7 24.9 - - + +
13B GLY 3.1 17.4 + - - +
15B GLY* 1.3 75.4 - - - +
17B THR* 1.3 60.2 + - - +
19B ALA* 4.2 1.8 - - - -
20B THR* 2.8 36.6 + - - -
11D ALA* 5.7 0.2 - - - -
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.8 21.1 + - - +
13B GLY 5.5 0.2 + - - -
14B PRO 3.6 12.7 + - - -
15B GLY 3.3 0.2 - - - -
16B ALA* 1.3 80.6 - - - +
18B ASN* 1.3 62.6 + - - +
20B THR* 3.9 2.3 - - - -
21B ILE* 3.2 31.7 + - + +
62B HIS* 3.9 25.6 - - + -
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Residues in contact with ASN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLY* 3.6 10.6 + - - +
16B ALA 3.3 0.4 - - - -
17B THR* 1.3 78.8 - - - +
19B ALA* 1.3 64.5 + - - +
21B ILE* 3.4 4.9 + - - +
22B ASN* 3.2 32.1 + - - +
62B HIS* 3.7 26.2 + - + +
77B ARG* 3.0 30.2 + - - +
11D ALA 5.7 3.0 + - - -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.5 6.0 - - + -
39A ALA* 3.6 29.2 - - + -
15B GLY 3.3 12.7 + - - +
16B ALA* 3.1 8.8 + - - +
18B ASN* 1.3 79.4 - - - +
20B THR* 1.3 57.1 + - - +
22B ASN* 3.5 2.5 + - - +
23B PHE* 2.9 29.1 + - - +
84B MET* 4.1 11.3 - - + +
11D ALA* 3.6 18.8 - - + +
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Residues in contact with THR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 4.1 7.4 - - - -
39A ALA 2.9 21.7 + - - -
40A LEU* 3.4 19.2 - - + -
41A ASP* 3.0 39.0 + - - +
47A ARG* 4.0 6.3 - - - +
16B ALA 2.8 14.9 + - - -
17B THR 3.9 0.7 - - - -
19B ALA* 1.3 72.0 - - - +
21B ILE* 1.3 60.3 + - - +
23B PHE* 4.2 0.4 - - + -
24B GLU* 2.8 52.2 + - + +
58B ARG* 4.1 2.0 - - - +
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 3.2 22.3 + - + +
18B ASN* 3.4 7.6 + - - +
20B THR* 1.3 76.0 - - - +
22B ASN* 1.3 58.9 + - - +
25B ALA* 2.9 26.3 + - - +
55B LEU* 3.6 15.9 - - + +
58B ARG* 4.1 33.0 - - + +
59B ILE* 3.8 16.2 - - + +
62B HIS* 3.7 41.7 - - + +
77B ARG* 3.7 26.9 - - - +
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Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASN* 3.2 24.2 + - - +
19B ALA* 3.9 3.3 - - - +
21B ILE* 1.3 75.1 - - - +
23B PHE* 1.3 66.0 + - - +
25B ALA* 3.1 7.7 + - - +
26B GLY 3.0 17.7 + - - -
72B MET* 5.6 0.2 - - - +
77B ARG* 2.8 46.1 + - - +
80B ILE* 3.5 42.8 - - + +
81B GLY* 3.0 12.1 + - - +
84B MET* 4.5 9.2 - - + +
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A CYS 3.6 17.0 - - - -
31A TYR* 3.6 37.7 - + - -
34A PHE* 3.5 50.7 - + + -
40A LEU* 4.8 1.3 - - + -
19B ALA 2.9 19.0 + - - +
20B THR 3.7 3.1 - - - +
22B ASN* 1.3 75.2 - - - +
24B GLU* 1.3 66.9 + - + +
26B GLY 3.0 14.9 + - - -
27B ILE* 3.0 32.6 + - + +
81B GLY* 4.3 3.1 - - - -
84B MET* 4.1 11.6 - - + -
85B MET* 3.3 33.7 - - + +
88B LEU* 3.7 11.7 - - + -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 2.6 41.5 + - + +
44A GLY* 4.6 0.5 - - - -
47A ARG* 2.6 38.7 + - - -
20B THR* 2.8 25.8 + - + +
23B PHE* 1.3 76.9 - - + +
25B ALA* 1.3 60.5 - - - +
26B GLY 3.1 0.2 - - - -
27B ILE* 3.4 8.6 - - + +
28B LEU* 2.9 27.9 + - - +
51B LEU* 3.9 13.2 - - + +
55B LEU* 3.9 6.6 - - + +
58B ARG* 2.5 40.1 + - - +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 2.9 21.3 + - + +
22B ASN* 3.1 11.6 + - - +
24B GLU* 1.3 77.9 - - - +
26B GLY* 1.3 57.3 + - - +
28B LEU* 3.6 3.1 + - - +
29B GLU 3.3 18.2 + - - -
55B LEU* 3.4 19.3 - - + +
74B LEU* 4.3 6.7 - - + -
77B ARG* 4.1 7.9 - - + -
78B LYS* 3.5 35.0 - - - +
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN 3.0 6.3 + - - -
23B PHE 3.0 8.2 + - - -
25B ALA* 1.3 76.3 - - - +
27B ILE* 1.3 63.7 + - - +
28B LEU 3.2 0.4 - - - -
29B GLU* 3.3 3.5 + - - +
30B CYS* 3.1 27.9 + - - -
78B LYS 4.3 0.7 - - - -
81B GLY* 3.8 24.6 - - - -
82B VAL* 3.9 11.4 - - - +
85B MET* 3.4 6.5 - - - -
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.0 32.5 - - + -
30A CYS* 4.5 5.2 - - + -
31A TYR* 4.0 11.9 - - + +
85A MET* 4.7 1.1 - - + -
23B PHE* 3.0 40.8 + - + +
24B GLU* 3.4 11.7 - - + +
26B GLY* 1.3 77.6 - - - +
28B LEU* 1.3 56.4 + - - +
30B CYS* 3.1 6.7 + - - +
31B TYR* 2.9 50.7 + - + -
51B LEU* 4.2 8.5 - - + -
85B MET* 3.7 24.5 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU 2.9 16.7 + - - +
25B ALA 3.6 6.5 - - - +
26B GLY 3.2 0.2 - - - -
27B ILE* 1.3 75.1 - - - +
29B GLU* 1.3 59.3 + - - +
31B TYR* 3.1 3.7 + - + +
32B GLU* 2.9 48.9 + - - +
48B LEU* 3.4 44.0 - - + +
51B LEU* 3.7 16.6 - - + +
52B LYS* 3.8 30.5 - - + +
55B LEU* 4.0 15.7 - - + -
74B LEU* 4.4 6.3 - - + -
78B LYS* 4.3 14.4 - - - -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 5.3 0.7 - - + -
25B ALA 3.3 12.5 + - - +
26B GLY 3.3 9.6 + - - +
28B LEU* 1.3 78.8 - - - +
30B CYS* 1.3 56.9 + - - +
32B GLU* 4.0 2.9 - - - +
33B ARG* 2.9 69.5 + - - +
75B GLU* 5.0 3.2 - - - +
78B LYS* 3.2 30.1 + - + +
82B VAL* 3.9 18.6 - - + -
77C LYS* 3.0 36.0 + - - -
80C GLU* 5.3 1.6 - - - +
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Residues in contact with CYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.4 17.5 - - + -
27A ILE* 4.6 1.1 - - + -
85A MET* 3.7 31.9 - - + -
88A LEU* 3.8 6.9 - - + +
89A LEU* 3.4 33.2 - - - -
26B GLY 3.1 21.7 + - - -
27B ILE* 3.1 10.2 + - - +
28B LEU 3.0 0.6 - - - -
29B GLU* 1.3 76.1 - - - +
31B TYR* 1.3 59.8 + - - +
33B ARG* 4.6 4.9 - - - +
34B PHE* 2.9 31.0 + - - +
85B MET* 4.4 2.5 - - - -
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Residues in contact with TYR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.8 20.0 - + - -
24A GLU* 2.6 42.6 + - + +
27A ILE* 4.1 14.8 - - + +
51A LEU* 4.3 11.6 - - - +
27B ILE* 2.9 44.1 + - + +
28B LEU* 3.1 11.2 + - - +
30B CYS* 1.3 76.5 - - - +
32B GLU* 1.3 56.4 + - - +
34B PHE* 3.2 3.3 + - - +
35B SER* 2.8 28.9 + - - -
40B LEU* 4.1 16.8 - - + +
44B GLY 4.2 9.9 - - - -
47B ARG* 4.6 8.1 + - + +
48B LEU* 3.6 37.5 - - + +
51B LEU* 4.6 7.2 - - + -
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 2.9 34.6 + - + +
29B GLU* 3.7 1.9 - - - +
31B TYR* 1.3 75.4 - - - +
33B ARG* 1.3 58.6 + - - +
35B SER* 2.9 18.0 + - - -
36B TRP* 3.0 23.4 - - + +
48B LEU* 3.7 24.8 - - + +
52B LYS* 4.1 19.6 + - - +
78B LYS* 3.1 24.6 + - - -
77C LYS* 2.7 39.2 + - + +
79C ASP* 5.2 4.0 - - - +
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 2.8 47.3 + - + -
89A LEU* 3.5 18.2 + - - +
91A MET* 3.3 27.5 - - - +
29B GLU* 2.9 54.2 + - - +
30B CYS* 4.0 5.8 - - - +
32B GLU* 1.3 78.1 - - - +
34B PHE* 1.3 61.1 + - - +
36B TRP* 3.4 9.9 + - - +
37B GLN* 2.8 29.1 + - - +
82B VAL* 4.7 8.7 - - - +
75C VAL 5.5 1.8 - - - +
76C ASP* 5.6 3.0 + - - +
77C LYS* 3.7 21.8 - - + -
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Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.6 16.2 - - + -
20A THR* 4.2 4.5 - - - -
23A PHE* 3.5 54.7 - + + -
84A MET* 4.1 13.0 - - + -
88A LEU* 3.7 17.4 - - + +
30B CYS 2.9 20.5 + - - +
31B TYR 3.4 3.8 - - - +
33B ARG* 1.3 76.9 - - - +
35B SER* 1.3 62.2 + - - +
37B GLN* 2.9 21.7 + - - +
39B ALA* 3.3 46.2 + - + -
40B LEU* 3.9 18.8 - - + -
10C LEU* 3.9 18.6 - - + -
11C ALA* 4.9 0.2 - - + -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.4 27.6 - - - +
12A VAL* 5.7 0.5 - - - +
31B TYR 2.8 14.3 + - - -
32B GLU* 2.9 12.9 + - - -
34B PHE* 1.3 78.2 - - - +
36B TRP* 1.3 59.5 + - - +
38B ARG* 3.2 14.6 + - - -
40B LEU* 3.9 15.3 + - - -
45B GLN* 3.9 21.1 + - - +
48B LEU* 3.9 15.9 - - - +
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Residues in contact with TRP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.2 20.5 - - + +
32B GLU* 3.0 29.0 + - - +
33B ARG* 3.9 4.9 - - - +
34B PHE 3.2 1.0 - - - -
35B SER* 1.3 76.6 - - - +
37B GLN* 1.3 59.9 + - - +
38B ARG* 3.1 20.9 + - - +
39C HIS* 5.4 4.0 - + - -
42C GLN* 3.6 25.1 - - - -
75C VAL* 3.2 46.9 - - + +
77C LYS* 3.2 39.8 - - + +
79C ASP* 4.3 14.7 + - + -
101C THR* 4.0 25.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il