Contacts of the helix formed by residues 12 - 29 (chain B) in PDB entry 1EQB
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 ASP 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ARG* 2.3 40.7 + - - -
274A VAL* 4.3 6.3 - - + -
277A LYS* 3.7 11.4 - - + +
8B ILE* 2.7 23.6 + - + +
11B TYR* 1.3 87.7 - - + +
13B ALA* 1.3 56.9 + - - +
14B GLU* 3.7 6.2 + - - +
15B LEU* 3.0 30.7 + - - +
16B TRP* 3.1 26.7 + - - +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA 4.2 10.6 + - - +
10B ASP 5.6 0.2 - - - -
11B TYR 4.0 1.0 - - - -
12B ASP* 1.3 71.6 + - - +
14B GLU* 1.3 58.5 + - - +
16B TRP* 3.9 8.4 - - + -
17B GLN* 2.8 36.2 + - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 5.0 6.2 - - - +
77A LEU* 3.4 33.4 - - + +
81A ARG* 4.5 3.6 - - - +
12B ASP* 3.3 9.1 + - - +
13B ALA* 1.3 81.3 - - - +
15B LEU* 1.3 64.7 + - - +
17B GLN* 3.4 9.4 + - - +
18B ALA* 3.4 12.3 + - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 5.5 0.4 - - + -
74A VAL* 3.9 31.6 - - + -
77A LEU* 3.4 20.7 - - + +
81A ARG* 4.2 0.2 - - - +
270A ALA* 3.4 30.7 - - + +
273A ALA* 4.1 6.5 - - + -
274A VAL* 3.6 20.6 - - + +
8B ILE* 4.3 12.8 - - + -
12B ASP* 3.0 28.9 + - - +
13B ALA 3.4 0.2 - - - -
14B GLU* 1.3 80.4 - - - +
16B TRP* 1.3 62.1 - - - +
18B ALA* 3.4 4.5 + - - +
19B MET* 3.1 37.8 + - + +
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Residues in contact with TRP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN* 3.5 25.6 - - + -
8B ILE* 3.9 22.6 - - + +
9B ALA* 3.6 36.9 - - + +
12B ASP 3.1 20.5 + - - +
13B ALA* 3.6 8.7 - - + +
14B GLU 3.2 0.2 - - - -
15B LEU* 1.3 74.2 - - - +
17B GLN* 1.3 69.8 + - - +
19B MET* 3.1 20.5 + - + +
20B GLU* 3.0 58.5 + - + +
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 6.0 1.8 - - - +
13B ALA 2.8 20.7 + - - +
14B GLU* 3.9 4.7 - - - +
16B TRP* 1.3 78.1 - - - +
18B ALA* 1.3 63.3 + - - +
20B GLU* 3.2 6.6 + - - +
21B GLN* 2.9 51.8 + - + +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A TYR* 3.6 22.3 - - - +
73A ILE* 3.6 34.3 - - + -
74A VAL* 4.0 10.3 - - + -
14B GLU 3.4 5.3 + - - +
15B LEU* 3.4 9.6 + - - +
16B TRP 3.3 0.6 - - - -
17B GLN* 1.3 77.9 - - - +
19B MET* 1.3 62.6 + - - +
21B GLN* 3.2 15.3 + - - +
22B GLU* 3.1 18.2 + - - +
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Residues in contact with MET 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLN* 4.8 1.3 - - + +
46A ALA* 4.0 16.2 - - + +
49A SER* 3.4 36.8 - - - +
51A LEU* 4.2 23.0 - - + +
74A VAL* 4.9 2.0 - - + -
270A ALA* 4.6 4.7 - - - -
8B ILE* 4.1 21.1 - - + -
15B LEU* 3.1 37.8 + - + +
16B TRP* 3.5 25.4 - - + +
18B ALA* 1.3 77.6 - - - +
20B GLU* 1.3 65.5 + - - +
22B GLU* 2.9 19.8 + - - +
23B LYS* 3.0 11.9 + - - +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 3.0 59.0 + - + +
17B GLN* 3.6 9.4 - - + +
19B MET* 1.3 77.3 - - - +
21B GLN* 1.3 62.9 + - + +
23B LYS* 3.1 51.4 + - - +
24B VAL* 3.1 14.6 + - + +
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.4 47.1 + - + -
73A ILE* 4.4 7.1 - - - +
17B GLN* 2.9 45.9 + - + +
18B ALA* 3.6 9.6 - - - +
19B MET 3.1 0.2 - - - -
20B GLU* 1.3 74.0 - - + +
22B GLU* 1.3 55.3 + - - +
24B VAL* 3.1 8.1 + - - +
25B ARG* 2.8 34.7 + - - +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLN* 5.3 0.9 - - + -
51A LEU* 3.3 31.2 - - + -
54A LYS* 3.8 10.6 - - - +
67A GLY 4.2 1.9 - - - +
70A TYR* 3.9 19.9 - - + +
71A VAL* 4.2 8.9 - - + +
18B ALA 3.1 11.1 + - - +
19B MET 2.9 10.2 + - - +
21B GLN* 1.3 76.7 - - - +
23B LYS* 1.3 56.0 + - - +
25B ARG* 2.5 40.8 + - - -
26B GLN* 2.7 58.7 + - - +
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 3.6 31.6 + - - +
50A GLN* 3.7 32.7 + - + +
19B MET 3.0 10.0 + - - +
20B GLU* 3.1 44.8 + - - +
22B GLU* 1.3 80.9 - - - +
24B VAL* 1.3 60.4 + - + +
26B GLN* 3.8 4.5 + - - +
27B GLU* 3.7 21.0 + - + +
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 3.1 13.4 + - + +
21B GLN* 3.1 10.1 + - - +
23B LYS* 1.3 79.5 - - + +
25B ARG* 1.3 61.0 + - - +
26B GLN 3.2 0.2 - - - -
27B GLU* 2.9 9.4 + - + +
28B GLU* 2.8 56.0 + - + +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 3.6 14.4 - - - +
67A GLY* 3.1 28.5 + - - -
69A GLU* 3.8 12.6 - - - +
70A TYR* 3.8 20.4 - - + -
21B GLN 2.8 16.7 + - - +
22B GLU* 2.5 52.1 + - - +
24B VAL* 1.3 76.2 - - - +
26B GLN* 1.3 76.1 + - - +
28B GLU* 4.4 3.4 - - - +
29B HIS* 2.9 65.3 + - + +
31B GLU* 2.6 39.5 + - - +
36B GLU* 4.7 0.8 + - - -
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLN* 2.8 48.7 + - - +
51A LEU* 4.7 1.0 - - - +
53A ASN* 3.1 28.5 + - - +
54A LYS* 4.7 3.2 - - - +
22B GLU* 2.7 47.6 + - - +
23B LYS 3.9 6.5 - - - +
24B VAL 3.2 0.2 - - - -
25B ARG* 1.3 90.7 - - - +
27B GLU* 1.3 59.9 + - + +
29B HIS* 4.0 3.0 - - - +
31B GLU* 5.6 0.7 - - - -
38B TYR* 3.7 21.6 + - + -
372B ARG* 3.9 3.3 + - - -
415B VAL* 3.3 21.1 - - + +
416B TYR* 4.1 2.4 - - - -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG* 5.0 5.1 + - - +
50A GLN* 6.0 0.7 - - - +
23B LYS 3.7 13.2 - - - +
24B VAL* 2.9 13.2 + - + +
26B GLN* 1.3 80.7 - - + +
28B GLU* 1.3 62.7 + - + +
29B HIS 3.3 0.9 - - - -
372B ARG* 2.5 28.7 + - - +
410B CYS* 3.3 11.4 - - - +
414B PRO* 3.4 15.6 - - - +
415B VAL* 3.0 24.4 + - - +
416B TYR* 3.0 38.3 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 2.8 43.6 + - + +
25B ARG* 3.3 2.3 + - - -
27B GLU* 1.3 75.8 - - + +
29B HIS* 1.3 62.5 + - + +
341B ASN* 2.8 30.8 + - - +
406B VAL* 4.0 0.2 - - - +
407B LEU* 3.7 25.4 - - + +
410B CYS* 3.8 14.2 - - - -
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Residues in contact with HIS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY* 5.1 2.0 - - - -
69A GLU* 4.4 10.5 - - - -
25B ARG* 2.9 47.4 + - + +
26B GLN 4.0 4.9 - - - +
27B GLU 3.3 0.2 - - - -
28B GLU* 1.3 84.1 - - + +
30B ILE* 1.3 62.7 + - - +
31B GLU* 3.4 18.0 + - + +
38B TYR* 4.2 1.6 + - - -
338B GLY* 4.8 6.5 - - - -
341B ASN* 3.3 46.1 + - - +
343B THR* 3.2 21.9 + - - +
372B ARG* 2.8 23.7 + - - -
410B CYS* 4.0 2.0 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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