Contacts of the helix formed by residues 20 - 39 (chain B) in PDB entry 4XHW
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 PHE 20 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 3.1 44.2 + - + +
16B HIS 4.2 0.4 + - - -
18B GLU* 4.1 21.5 - - + -
19B GLY* 1.3 78.9 - - - +
21B SER* 1.3 57.1 + - - +
22B ILE 3.3 2.7 - - - -
23B PRO* 3.1 14.1 - - + +
24B LEU* 2.8 35.9 + - + +
55B GLU* 5.3 3.4 - - + -
58B GLU* 4.9 14.1 - - + -
59B ALA* 4.0 37.7 - - + -
62B ASN* 3.7 30.3 - - + -
65B PHE* 4.6 6.3 - + + -
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU 4.7 0.4 + - - -
16B HIS* 3.2 40.9 + - - +
19B GLY* 3.3 7.2 + - - -
20B PHE* 1.3 78.3 - - - +
22B ILE* 1.3 63.5 + - - +
24B LEU* 3.3 6.1 + - - +
25B LEU* 2.9 30.0 + - - +
37C ASP* 5.7 2.4 + - - -
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY 4.8 0.8 + - - -
21B SER* 1.3 77.8 + - - +
23B PRO* 1.4 75.8 - - + +
25B LEU* 3.1 13.5 + - + +
26B TRP* 3.0 20.7 + - + +
53B THR* 5.9 0.7 - - - +
55B GLU* 3.9 21.3 - - + +
56B ASN* 4.3 10.3 - - - +
52D LEU* 3.9 24.8 - - + +
53D THR* 4.6 18.6 - - + -
54D GLU 6.0 0.4 - - - +
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Residues in contact with PRO 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.1 28.9 - - + +
22B ILE* 1.4 88.8 - - + +
24B LEU* 1.3 55.3 + - - +
26B TRP* 3.1 12.0 + - + +
27B LEU* 2.9 26.2 + - - +
55B GLU* 3.7 22.7 - - + +
56B ASN* 3.7 21.8 - - - +
59B ALA* 3.6 32.1 - - + -
65B PHE* 4.0 12.2 - - + -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN 4.0 8.7 - - - +
15B LEU* 4.2 6.3 - - + -
16B HIS* 3.5 51.6 - - + +
20B PHE* 2.8 30.2 + - + +
21B SER* 3.5 5.6 - - - +
22B ILE 3.2 0.2 - - - -
23B PRO* 1.3 72.1 - - - +
25B LEU* 1.3 57.8 + - - +
27B LEU* 3.1 10.0 + - + +
28B GLN* 2.9 30.4 + - - +
65B PHE* 3.6 24.0 - - + -
68B LEU* 3.8 23.1 - - + -
103B LEU* 4.1 16.2 - - + +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER 2.9 17.6 + - - +
22B ILE* 3.1 13.2 + - + +
24B LEU* 1.3 75.3 - - - +
26B TRP* 1.3 64.1 + - - +
28B GLN* 3.3 14.6 + - - +
29B ASN* 2.9 21.8 + - - +
50C VAL* 4.2 32.5 - - + +
52C LEU* 4.1 21.0 - - + +
52D LEU* 3.8 39.5 - - + +
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Residues in contact with TRP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.0 11.7 + - + +
23B PRO* 3.2 20.6 - - + +
25B LEU* 1.3 76.2 - - - +
27B LEU* 1.3 70.5 + - + +
29B ASN* 2.9 13.8 + - + +
30B CYS* 3.0 30.0 + - - -
49B LEU* 4.0 17.5 - - + -
50B VAL 3.2 36.1 + - - -
51B PRO* 3.9 4.5 - - + -
52B LEU* 6.1 1.6 - - - +
56B ASN* 3.3 36.5 - - + +
60B MSE 3.1 40.4 - - + -
65B PHE* 4.8 7.6 - + - -
52D LEU* 3.8 28.6 - - + +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO 2.9 12.5 + - - +
24B LEU* 3.1 8.9 + - + +
26B TRP* 1.3 82.0 - - + +
28B GLN* 1.3 59.4 + - - +
30B CYS* 2.8 23.1 + - - +
31B LEU* 3.0 35.3 + - + +
49B LEU* 4.1 19.7 - - + -
65B PHE* 4.2 14.1 - - + -
68B LEU* 4.2 15.7 - - + -
69B LEU* 3.6 33.9 - - + -
72B LEU* 3.7 19.5 - - + -
74B VAL* 5.0 2.7 - - + -
103B LEU* 4.3 8.3 - - + -
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Residues in contact with GLN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU 2.9 12.3 + - - +
25B LEU* 3.4 19.8 - - - +
27B LEU* 1.3 78.8 - - - +
29B ASN* 1.3 62.1 + - - +
31B LEU* 3.4 2.6 + - - +
32B ILE* 3.0 32.7 + - + +
100B ALA* 3.0 40.5 + - + +
101B ALA* 4.6 4.2 - - - +
103B LEU* 3.8 18.6 - - + +
52C LEU* 3.5 24.3 - - + +
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Residues in contact with ASN 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU 2.9 11.9 + - - +
26B TRP* 2.9 10.1 + - - +
28B GLN* 1.3 76.7 - - - +
30B CYS* 1.3 66.4 + - - +
32B ILE* 4.6 2.7 - - - +
33B ARG* 2.8 72.6 + - - +
52C LEU* 3.8 24.1 - - + +
50D VAL* 3.9 15.9 + - - +
52D LEU* 4.1 20.0 - - + +
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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
----------------------------------------------------------
26B TRP* 3.0 42.0 + - - -
27B LEU* 2.8 10.1 + - - +
29B ASN* 1.3 80.5 - - - +
31B LEU* 1.3 61.5 + - + +
33B ARG* 4.0 3.6 - - - +
34B ALA* 3.0 26.3 + - - +
47B VAL* 5.4 8.3 - - + +
48B PRO 5.6 2.0 - - - -
49B LEU* 3.7 32.8 - - + -
87B ILE* 4.0 7.8 - - + +
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Residues in contact with LEU 31 (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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27B LEU* 3.0 36.0 + - + +
28B GLN* 3.7 6.3 - - - +
30B CYS* 1.3 75.9 - - - +
32B ILE* 1.3 59.1 + - - +
34B ALA* 3.4 3.3 + - - +
35B ALA* 3.0 26.9 + - - +
72B LEU* 4.3 12.6 - - + +
74B VAL* 5.1 6.3 - - + -
87B ILE* 3.8 20.9 - - + -
91B LEU* 5.9 0.4 - - + -
96B LEU* 3.7 42.3 - - + +
99B ALA* 4.0 14.6 - - + -
100B ALA* 3.9 26.7 - - + +
103B LEU* 4.8 1.6 - - + -
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLN* 3.0 30.4 + - + +
29B ASN* 4.0 2.9 - - - +
30B CYS 3.3 0.2 - - - -
31B LEU* 1.3 75.3 - - - +
33B ARG* 1.3 76.1 + - - +
35B ALA* 3.3 9.1 + - - +
36B ASP* 3.1 24.0 + - - +
97B ARG* 4.6 17.3 - - + +
100B ALA* 3.8 22.9 - - + -
52C LEU* 3.5 44.6 - - + +
53C THR* 4.3 18.6 - - + -
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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
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29B ASN* 2.8 66.2 + - - +
30B CYS* 4.2 3.6 - - - +
32B ILE* 1.3 88.2 - - - +
34B ALA* 1.3 63.2 + - - +
36B ASP* 3.0 30.4 + - - +
37B ASP* 3.0 29.9 + - - +
52C LEU* 2.7 32.1 + - - +
53C THR* 4.4 4.6 - - - +
54C GLU* 4.6 4.6 - - - +
47D VAL* 5.4 6.5 - - + -
48D PRO* 3.5 42.2 - - - +
50D VAL* 4.4 7.3 - - - +
84D PHE* 5.9 0.8 - - - -
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Residues in contact with ALA 34 (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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30B CYS 3.0 18.3 + - - +
31B LEU* 3.5 7.2 - - - +
33B ARG* 1.3 76.4 - - - +
35B ALA* 1.3 62.6 + - - +
37B ASP* 3.2 8.7 + - - +
38B ARG* 3.0 32.8 + - - +
47B VAL* 4.4 24.2 - - + -
87B ILE* 4.5 7.4 - - + -
96B LEU* 3.9 15.3 - - + -
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Residues in contact with ALA 35 (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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31B LEU 3.0 13.9 + - - +
32B ILE 3.5 9.0 - - - +
33B ARG 3.3 0.2 - - - -
34B ALA* 1.3 76.3 - - - +
36B ASP* 1.3 63.2 + - - +
38B ARG* 3.0 13.2 + - - +
39B GLU* 3.1 16.1 + - - +
93B PRO* 3.8 24.9 - - + +
96B LEU* 3.8 11.6 - - + +
97B ARG* 3.6 30.5 - - + +
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Residues in contact with ASP 36 (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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32B ILE* 3.1 12.2 + - - +
33B ARG* 3.0 38.5 + - - +
35B ALA* 1.3 77.5 - - - +
37B ASP* 1.3 66.2 + - - +
39B GLU* 3.5 11.6 + - - +
97B ARG* 2.9 31.2 + - - +
53C THR* 5.6 0.3 - - - -
54C GLU* 4.7 18.7 + - - +
45D GLN* 3.3 26.9 + - - +
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Residues in contact with ASP 37 (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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33B ARG* 3.0 15.2 + - - +
34B ALA* 3.2 9.6 + - - +
36B ASP* 1.3 79.7 - - - +
38B ARG* 1.3 61.9 + - + +
39B GLU 3.2 1.7 + - - -
40B GLU* 3.7 8.0 + - - +
43B CYS* 3.5 26.2 - - + +
37D ASP* 2.6 33.9 - - + +
45D GLN* 4.4 25.2 + - + +
46D ALA 5.5 0.7 - - - +
47D VAL* 4.9 14.8 - - - +
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.0 17.9 + - - +
35B ALA 3.0 5.7 + - - +
37B ASP* 1.3 76.4 - - + +
39B GLU* 1.3 62.9 + - - +
40B GLU 3.4 7.6 - - - +
41B ASP* 5.2 0.7 - - - -
43B CYS 3.4 20.6 - - - +
44B SER* 3.7 14.8 + - - +
45B GLN 2.9 29.8 + - - +
47B VAL* 4.5 5.1 - - - +
87B ILE* 3.2 19.0 + - - +
88B PRO 2.9 29.2 + - - -
89B ALA* 3.6 7.5 + - - +
91B LEU* 2.9 32.9 + - - +
93B PRO* 3.7 21.2 - - + +
96B LEU* 3.3 28.9 - - - +
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Residues in contact with GLU 39 (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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35B ALA 3.1 13.4 + - - +
36B ASP* 3.8 10.5 - - - +
37B ASP 3.2 1.6 - - - -
38B ARG* 1.3 76.3 - - - +
40B GLU* 1.3 64.8 + - - +
41B ASP* 3.5 7.8 + - - +
93B PRO* 3.6 18.9 - - - +
97B ARG* 2.9 28.4 + - - +
45D GLN* 5.0 3.6 - - - +
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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