Contacts of the strand formed by residues 50 - 57 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA* 3.6 5.8 - - + +
27A VAL* 4.3 21.8 - - + -
44A LEU* 3.5 39.3 - - + +
47A SER* 3.3 17.1 + - - +
48A PRO 3.3 0.4 - - - -
49A LEU* 1.3 81.9 - - + +
51A SER* 1.3 60.5 + - - +
52A ARG 3.5 26.2 - - - +
53A LEU* 4.3 9.0 - - + -
74A LYS* 3.8 11.7 - - - -
75A ALA* 3.3 24.6 + - + +
259A VAL* 5.6 1.1 - - + -
260A PHE* 4.5 4.3 - - + -
263A VAL* 6.0 1.3 - - + -
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASN* 3.0 38.7 + - - +
25A ALA 2.9 9.3 + - - +
26A LYS* 4.3 9.7 + - - +
49A LEU 4.0 0.2 + - - -
50A VAL* 1.3 73.9 - - - +
52A ARG* 1.3 63.4 + - - +
74A LYS* 4.1 15.6 - - - +
75A ALA* 3.4 6.9 - - - +
76A ALA* 3.0 20.6 + - - +
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA 3.4 1.4 + - - -
26A LYS* 3.4 40.8 - - + +
27A VAL 2.9 27.6 + - - +
50A VAL* 3.5 7.6 - - - +
51A SER* 1.3 82.3 + - - +
53A LEU* 1.3 63.8 + - - +
54A THR* 3.7 24.9 - - + +
76A ALA* 3.5 18.8 - - + +
78A LYS* 6.1 3.8 - - + -
88A ASP 5.6 2.3 + - - -
89A CYS 4.4 0.8 + - - -
91A LYS 3.0 28.3 + - - -
92A GLY* 3.7 4.0 - - - -
93A CYS* 3.3 32.7 - - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.4 16.8 - - + +
29A VAL* 4.0 13.5 - - + -
41A SER* 3.4 26.0 - - - +
44A LEU* 3.8 30.3 - - + -
45A LYS* 3.9 21.1 - - + +
50A VAL* 4.3 7.6 - - + -
52A ARG* 1.3 72.5 - - - +
54A THR* 1.3 62.2 + - - +
55A LEU* 3.7 17.7 - - + -
68A LEU* 4.6 5.4 - - + -
75A ALA* 4.7 3.6 - - + -
76A ALA 2.8 14.7 + - - +
77A VAL* 3.3 13.7 - - + +
78A LYS 3.0 24.8 + - - +
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL 3.0 6.7 + - - +
28A ALA* 3.2 13.9 - - - +
29A VAL* 2.9 25.8 + - - +
52A ARG* 3.7 32.1 - - + +
53A LEU* 1.3 75.9 - - - +
55A LEU* 1.3 63.5 + - - +
78A LYS* 3.5 7.9 - - + -
80A TYR* 3.7 24.2 - - + +
88A ASP 5.1 0.9 - - - +
89A CYS* 2.7 35.2 + - - +
93A CYS* 3.8 3.1 - - - -
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.7 9.0 - - + -
32A ALA* 3.6 12.3 - - + -
41A SER* 3.3 22.9 - - - +
53A LEU* 3.7 23.1 - - + -
54A THR* 1.3 78.1 - - - +
56A TYR* 1.3 57.4 + - - +
61A THR* 3.4 9.1 - - + +
64A VAL* 3.9 18.2 - - + -
65A ALA* 4.1 9.2 - - - +
68A LEU* 3.8 25.8 - - + -
77A VAL* 3.9 19.1 - - + -
78A LYS 2.8 15.7 + - - +
79A GLY* 4.4 0.9 - - - -
80A TYR* 2.7 35.7 + - - -
89A CYS* 3.8 1.3 - - - -
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Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL 2.9 7.9 + - - -
30A LEU* 3.7 25.4 - - + -
31A GLY 2.8 31.6 + - - -
32A ALA* 3.0 7.3 + - - +
55A LEU* 1.3 75.0 - - - +
57A ASP* 1.3 74.1 + - - +
58A ILE* 4.0 13.0 - - + +
61A THR* 3.9 2.9 - - - -
80A TYR* 3.6 15.9 - - + -
81A LEU 4.2 0.4 - - - -
82A GLY* 3.1 48.8 - - - -
83A PRO* 3.2 9.9 - - - +
86A LEU* 3.8 42.1 - - + +
89A CYS* 3.7 8.7 - - - -
124A LEU* 4.2 17.7 - - + -
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Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLY* 3.2 18.0 - - - +
33A SER* 3.0 37.8 + - - +
34A GLY* 3.7 4.3 + - - -
56A TYR* 1.3 86.4 - - - +
58A ILE* 1.3 87.3 + - - +
59A ALA 3.3 16.1 + - - +
61A THR* 3.5 10.3 + - + +
80A TYR 3.4 5.1 + - - +
81A LEU* 3.5 1.9 - - - -
82A GLY 3.3 19.1 + - - -
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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