Contacts of the strand formed by residues 50 - 57 (chain B) in PDB entry 4WLE
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 VAL 50 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA* 3.8 6.3 - - + +
27B VAL* 4.2 21.8 - - + -
44B LEU* 3.5 38.8 - - + +
47B SER* 3.3 13.7 + - - +
48B PRO 3.2 0.4 - - - -
49B LEU* 1.3 82.5 - - + +
51B SER* 1.3 60.9 + - - +
52B ARG 3.5 26.9 - - - +
53B LEU* 4.3 10.1 - - + -
74B LYS* 3.1 13.4 + - - -
75B ALA* 3.3 24.3 + - + +
259B VAL* 5.8 1.1 - - + -
260B PHE* 4.6 3.6 - - + -
263B VAL* 5.8 2.7 - - + -
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN* 3.0 43.5 + - - -
25B ALA 3.0 5.5 + - - -
26B LYS* 4.7 1.6 - - - +
49B LEU 4.0 1.6 + - - -
50B VAL* 1.3 74.1 - - - +
52B ARG* 1.3 66.5 + - - +
74B LYS* 3.9 13.7 - - - +
75B ALA* 3.3 6.6 - - - +
76B ALA* 2.9 22.0 + - - +
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Residues in contact with ARG 52 (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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25B ALA 3.3 1.6 + - - -
26B LYS* 3.3 43.1 - - + +
27B VAL 2.9 26.8 + - - -
50B VAL* 3.5 7.4 - - - +
51B SER* 1.3 83.9 + - - +
53B LEU* 1.3 62.9 + - - +
54B THR* 3.5 26.2 + - + +
76B ALA* 3.5 17.7 - - + +
78B LYS* 6.0 5.4 - - + -
80B TYR* 5.7 1.4 + - - -
88B ASP 5.2 3.8 + - - -
89B CYS 3.9 2.2 + - - -
91B LYS 3.3 22.8 + - - -
92B GLY* 5.0 0.6 - - - -
93B CYS* 3.1 35.8 - - - +
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Residues in contact with LEU 53 (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 VAL* 3.4 20.4 - - + +
29B VAL* 4.0 23.3 - - + -
41B SER* 3.5 24.9 - - - +
44B LEU* 4.1 17.3 - - + -
45B LYS* 3.9 22.0 - - + +
50B VAL* 4.3 8.5 - - + -
52B ARG* 1.3 73.0 - - - +
54B THR* 1.3 61.4 + - - +
55B LEU* 3.8 18.6 - - + -
68B LEU* 4.9 2.5 - - + -
75B ALA* 4.7 3.6 - - + -
76B ALA 2.8 14.3 + - - +
77B VAL* 3.3 16.2 - - + +
78B LYS 3.1 24.1 + - - +
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Residues in contact with THR 54 (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 VAL 2.9 6.0 + - - +
28B ALA* 3.2 15.8 - - - +
29B VAL 2.8 26.5 + - - +
52B ARG* 3.5 35.2 - - + +
53B LEU* 1.3 75.3 - - - +
55B LEU* 1.3 65.2 + - - +
78B LYS* 3.5 7.9 - - + -
80B TYR* 3.8 23.1 - - + +
88B ASP 5.3 0.2 - - - +
89B CYS* 3.0 31.0 + - - +
93B CYS* 3.8 3.1 - - - -
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.7 11.2 - - + -
32B ALA* 3.6 9.2 - - + -
41B SER* 3.4 23.3 - - - +
53B LEU* 3.8 20.0 - - + -
54B THR* 1.3 82.1 - - - +
56B TYR* 1.3 58.2 + - - +
61B THR* 3.4 9.1 - - + +
64B VAL* 4.0 17.3 - - + -
65B ALA* 4.0 9.6 - - - +
68B LEU* 3.7 25.8 - - + -
77B VAL* 3.9 19.3 - - + -
78B LYS 2.9 13.1 + - - +
79B GLY* 4.4 1.3 - - - -
80B TYR* 2.7 35.0 + - - -
89B CYS* 4.0 1.3 - - - -
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Residues in contact with TYR 56 (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 VAL 2.9 6.7 + - - -
30B LEU* 3.7 24.9 - - + -
31B GLY 2.8 30.9 + - - -
32B ALA* 2.9 7.7 + - - +
55B LEU* 1.3 76.7 - - - +
57B ASP* 1.3 72.9 + - - +
58B ILE* 4.1 11.1 - - + +
61B THR* 3.7 2.7 - - - -
80B TYR* 3.5 15.0 - - + -
81B LEU 4.3 0.4 - - - -
82B GLY* 3.1 29.7 - - - -
83B PRO* 3.0 29.6 - - - +
86B LEU* 3.7 41.8 - - + +
89B CYS* 3.7 7.8 - - + -
124B LEU* 4.0 22.0 - - + -
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Residues in contact with ASP 57 (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 GLY* 3.2 17.5 - - - +
33B SER* 2.9 38.1 + - - +
34B GLY* 3.7 3.6 + - - -
56B TYR* 1.3 84.9 - - - +
58B ILE* 1.3 85.1 + - - +
59B ALA 3.3 16.7 + - - +
61B THR* 3.4 10.9 + - + +
80B TYR 3.3 5.3 + - - +
81B LEU* 3.5 2.3 - - - -
82B GLY 3.1 20.4 + - - -
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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
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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