Contacts of the helix formed by residues 15 - 31 (chain B) in PDB entry 4WB7
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 SER 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLY 3.7 1.5 + - - -
14B ALA* 1.3 75.9 - - - +
16B ASP* 1.3 61.6 + - - +
17B GLU* 3.9 7.9 + - - +
18B GLU* 3.1 35.0 + - - +
19B ILE* 2.8 30.4 + - - +
60B ARG* 4.9 0.7 - - - +
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Residues in contact with ASP 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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15B SER* 1.3 74.3 - - - +
17B GLU* 1.3 58.7 + - - +
19B ILE* 3.1 12.6 + - - +
20B LYS* 2.8 32.9 + - - +
54B LEU 4.8 4.5 - - - +
55B SER* 5.4 8.1 - - - +
57B PRO* 5.9 3.3 - - - +
60B ARG* 4.1 14.7 + - - -
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 4.2 7.4 - - - +
16B ASP* 1.3 80.7 - - - +
18B GLU* 1.3 57.0 + - + +
20B LYS* 3.5 28.9 + - - +
21B ARG* 3.1 61.2 + - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.8 8.4 - - + +
11B ALA* 6.0 0.5 - - - +
14B ALA* 3.3 17.4 - - + +
15B SER* 3.1 36.2 + - - +
17B GLU* 1.3 75.8 - - + +
19B ILE* 1.3 62.8 + - - +
21B ARG* 3.6 18.0 - - + +
22B ALA* 3.0 29.8 + - - +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 5.3 0.9 - - + -
8B LEU* 4.5 7.7 - - + +
10B LEU* 3.7 22.0 - - + -
14B ALA* 4.3 5.2 - - + -
15B SER 2.8 16.3 + - - +
16B ASP* 3.5 11.9 - - - +
18B GLU* 1.3 75.4 - - - +
20B LYS* 1.3 63.9 + - - +
22B ALA* 3.3 2.4 + - - +
23B TYR* 3.0 23.4 + - - +
51B TYR* 3.9 22.7 - - + -
54B LEU* 3.6 44.9 - - + +
55B SER* 4.4 7.9 - - - +
60B ARG* 3.8 28.3 - - - +
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Residues in contact with LYS 20 (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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16B ASP 2.8 15.4 + - - +
17B GLU* 3.5 32.3 + - - +
19B ILE* 1.3 79.2 - - - +
21B ARG* 1.3 60.3 + - - +
23B TYR* 3.4 4.0 + - - +
24B ARG* 3.2 51.6 + - + +
51B TYR* 4.3 26.4 - - + +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.1 51.4 + - - +
18B GLU* 3.6 22.1 - - + +
20B LYS* 1.3 74.4 - - - +
22B ALA* 1.3 69.2 + - + +
24B ARG* 3.8 10.7 - - - +
25B ARG* 3.0 29.3 + - - +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.8 14.4 - - + +
9B GLY 5.3 0.4 - - - +
10B LEU* 3.6 31.6 - - + -
18B GLU 3.0 19.1 + - - +
19B ILE 3.3 3.1 + - - +
21B ARG* 1.3 80.6 - - + +
23B TYR* 1.3 62.4 + - - +
25B ARG* 3.4 8.3 + - - +
26B GLN* 3.0 30.4 + - + +
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.1 12.2 - - + +
19B ILE 3.0 11.4 + - - +
20B LYS 3.8 3.1 - - - +
22B ALA* 1.3 78.2 - - - +
24B ARG* 1.3 68.1 + - + +
26B GLN* 3.4 0.9 + - - +
27B ALA* 2.8 51.7 + - + +
44B PHE* 4.8 12.3 + + - -
47B ILE* 3.5 27.8 - - + -
48B ALA* 3.8 23.1 - - + +
51B TYR* 3.7 53.4 - + + -
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 3.2 42.3 + - + +
21B ARG* 3.8 10.4 - - - +
22B ALA 3.3 0.2 - - - -
23B TYR* 1.3 87.9 - - + +
25B ARG* 1.3 63.6 + - - +
27B ALA* 3.2 4.4 + - - +
28B LEU* 3.0 35.2 + - + +
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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
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21B ARG* 3.0 22.2 + - - +
22B ALA* 3.5 9.0 - - - +
24B ARG* 1.3 78.4 - - - +
26B GLN* 1.3 76.9 + - - +
28B LEU* 3.5 10.6 + - + +
29B ARG* 3.4 17.7 + - - +
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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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7B THR 4.4 6.6 - - - +
8B LEU* 3.9 30.5 + - + +
9B GLY* 5.9 0.4 - - - -
22B ALA* 3.0 17.4 + - - +
23B TYR 4.0 2.0 - - - +
25B ARG* 1.3 94.9 - - + +
27B ALA* 1.3 62.8 + - - +
29B ARG* 3.1 55.3 + - - +
30B TYR* 3.4 21.7 + - - -
47B ILE* 3.6 23.4 - - + +
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Residues in contact with ALA 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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23B TYR* 2.8 49.5 + - + +
24B ARG* 3.5 5.2 - - - +
26B GLN* 1.3 72.7 - - - +
28B LEU* 1.3 66.1 + - + +
29B ARG 3.0 1.3 - - - -
30B TYR 3.0 2.6 + - - -
31B HIS* 3.0 22.4 + - + +
44B PHE* 3.5 23.4 - - + -
47B ILE* 4.3 4.9 - - + +
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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
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24B ARG* 3.0 27.1 + - + +
25B ARG* 3.8 9.4 - - + +
27B ALA* 1.3 75.5 - - + +
29B ARG* 1.3 62.3 + - - +
30B TYR 3.5 0.2 + - - -
31B HIS* 3.5 22.6 + - + +
34B LYS* 4.3 30.5 - - + +
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG 3.4 8.3 + - - +
26B GLN* 3.1 51.4 + - - +
28B LEU* 1.3 80.8 - - - +
30B TYR* 1.3 77.7 + - + +
34B LYS 5.3 0.5 - - - -
35B ASN* 3.0 25.6 + - - +
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Residues in contact with TYR 30 (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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26B GLN* 3.4 10.2 + - - +
27B ALA 3.0 5.4 + - - -
29B ARG* 1.3 102.3 + - + +
31B HIS* 1.3 66.5 + - - +
32B PRO* 3.3 3.8 - - - +
35B ASN* 3.5 31.3 - - - +
37B GLU* 6.1 0.7 - - - -
40B ALA* 4.0 23.3 - - - +
41B GLU* 5.7 0.2 - - - -
43B LYS* 3.4 47.4 + - + +
44B PHE* 3.6 24.5 - - + +
47B ILE* 3.5 31.9 - - + -
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Residues in contact with HIS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 3.0 13.6 + - + +
28B LEU* 3.5 19.2 + - + +
29B ARG 3.5 1.8 - - - -
30B TYR* 1.3 76.4 - - - +
32B PRO* 1.3 63.7 - - + +
33B ASP* 3.0 49.6 + - + +
34B LYS* 2.9 18.4 + - + +
35B ASN 2.7 33.1 + - - -
44B PHE* 3.8 21.0 - + - -
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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