Contacts of the strand formed by residues 113 - 121 (chain A) in PDB entry 1WL4
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 ILE 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 5.4 0.7 - - + -
47A VAL* 4.0 20.4 - - + -
51A ASP 3.7 19.5 - - - +
52A VAL* 3.8 11.0 - - + -
53A SER* 2.7 36.3 + - - -
54A GLU 3.7 0.3 + - - -
112A SER* 1.3 91.9 - - - +
114A VAL* 1.3 66.5 - - - +
262A VAL* 4.2 19.5 - - + -
263A LEU 3.3 10.8 - - - +
264A MET* 4.2 15.7 - - + -
268A GLU* 4.7 2.0 - - + +
272A ARG* 3.5 40.8 - - - +
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Residues in contact with VAL 114 (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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54A GLU* 3.4 21.1 - - + +
56A ILE* 4.0 15.9 - - + -
102A ALA* 3.6 26.9 - - + -
105A SER* 3.9 6.7 - - - +
106A ILE* 3.8 17.9 - - + -
111A SER* 3.7 24.7 - - - -
113A ILE* 1.3 78.7 - - - +
115A VAL* 1.3 77.1 + - - +
116A ALA* 3.8 0.9 + - + -
261A VAL 3.8 0.7 - - - +
262A VAL* 3.6 2.6 - - - +
263A LEU* 3.0 34.0 + - + +
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Residues in contact with VAL 115 (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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38A ILE* 4.1 26.2 - - + -
41A VAL* 4.1 16.4 - - + -
42A LEU* 3.8 35.0 - - + -
52A VAL* 4.1 14.8 - - + +
54A GLU 3.2 5.9 + - - -
55A VAL* 3.3 15.9 - - + +
56A ILE 3.0 24.3 + - - +
57A PHE* 4.3 2.7 - - + -
79A ILE* 4.7 0.7 - - + -
113A ILE* 5.5 0.4 - - + -
114A VAL* 1.3 75.2 - - - +
116A ALA* 1.3 61.4 + - - +
260A ALA* 4.2 7.0 - - + -
261A VAL 3.5 11.0 - - - +
262A VAL* 4.3 7.4 - - + -
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Residues in contact with ALA 116 (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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56A ILE 3.1 10.3 - - - +
57A PHE* 3.9 4.0 - - - -
98A ALA 3.8 21.5 - - - +
99A VAL* 3.9 17.9 - - + +
102A ALA* 4.2 13.0 - - + -
114A VAL* 3.8 3.2 + - + -
115A VAL* 1.3 75.0 - - - +
117A GLY* 1.3 58.9 + - - +
260A ALA* 3.2 4.3 - - - +
261A VAL* 2.8 40.4 + - + +
263A LEU* 5.0 2.2 - - + -
360A CYS* 4.7 0.2 - - - -
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Residues in contact with GLY 117 (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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56A ILE 3.1 7.3 + - - -
57A PHE* 3.2 12.5 - - - -
58A GLY 2.9 19.6 + - - -
95A GLY 3.8 3.6 + - - +
98A ALA* 3.3 10.3 - - - +
116A ALA* 1.3 78.3 - - - +
118A GLY* 1.3 58.5 + - - -
259A ALA 3.1 13.5 - - - -
360A CYS* 3.7 17.0 - - - -
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Residues in contact with GLY 118 (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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57A PHE* 3.5 5.5 - - - -
58A GLY 3.3 8.5 - - - -
95A GLY* 4.2 1.6 - - - -
117A GLY* 1.3 74.6 - - - -
119A MET* 1.3 62.7 + - - +
258A ALA* 3.2 3.1 - - - +
259A ALA 3.0 31.8 + - - +
356A GLY 3.2 17.3 - - - -
357A ALA* 3.6 10.4 - - - +
360A CYS* 3.9 4.6 - - - +
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A VAL* 3.6 31.0 - - + +
31A GLN* 4.4 3.4 - - - -
34A GLY* 4.2 9.6 - - - +
57A PHE* 4.0 17.3 - - + -
58A GLY 3.0 18.5 + - - +
59A HIS* 3.3 29.2 + - + +
69A PRO* 3.7 43.5 - - + +
70A VAL* 3.9 11.7 - - + -
73A ALA* 4.5 4.7 - - - -
118A GLY* 1.3 75.5 - - - +
120A GLU* 1.3 69.1 + - - +
257A GLY 3.5 6.5 - - - -
258A ALA* 3.9 13.7 - - + -
356A GLY* 3.6 4.0 + - - -
357A ALA* 4.0 2.9 - - - -
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Residues in contact with GLU 120 (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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30A VAL* 3.6 7.1 - - - +
33A LEU* 4.1 1.4 - - - +
59A HIS* 3.3 10.7 + - - -
60A VAL* 3.0 23.0 + - - +
61A LEU* 2.8 40.5 + - + +
119A MET* 1.3 75.9 - - - +
121A ASN* 1.3 62.8 + - - +
122A MET* 3.7 24.5 - - + +
256A ASP* 3.4 2.9 - - - +
257A GLY 2.9 34.6 + - - +
354A PRO* 3.8 14.8 - - + -
355A LEU* 3.8 6.7 - - + +
356A GLY* 2.8 31.5 + - - +
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Residues in contact with ASN 121 (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 LEU 3.1 20.0 + - - -
26A ALA 3.8 6.9 + - - -
28A VAL 2.7 26.0 + - - +
30A VAL* 3.6 27.7 - - + +
33A LEU* 4.3 5.6 - - + +
59A HIS* 5.2 0.6 - - - -
61A LEU* 5.2 5.0 - - - +
120A GLU* 1.3 80.4 + - - +
122A MET* 1.3 59.3 + - - +
123A SER* 3.0 10.6 + - - -
124A LYS* 2.9 37.1 + - + +
125A ALA* 3.6 8.5 + - - +
256A ASP* 3.2 9.8 + - - +
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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