Contacts of the strand formed by residues 34 - 46 (chain A) in PDB entry 1WCP
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A HIS* 3.7 38.8 - - + +
28A LYS* 3.9 15.0 - - + +
29A VAL* 3.9 5.8 - - + +
33A GLY* 1.3 73.5 - - - -
35A SER* 1.3 64.5 + - - +
36A TYR* 3.5 33.4 - - + +
109A THR* 3.5 5.4 - - - +
110A VAL* 3.2 33.6 + - + +
177A THR* 4.0 19.3 - - + -
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Residues in contact with SER 35 (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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34A VAL* 1.3 73.8 - - - +
36A TYR* 1.3 78.6 + - - +
107A THR* 4.5 15.2 - - - +
108A LEU 3.4 9.9 - - - -
109A THR* 3.2 21.2 + - - +
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Residues in contact with TYR 36 (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 HIS* 5.2 9.2 + - - +
34A VAL* 3.5 27.6 - - + +
35A SER* 1.3 84.5 - - - +
37A LEU* 1.3 61.0 + - - +
38A VAL* 3.6 15.8 + - + +
107A THR* 4.3 2.6 - - - -
108A LEU* 3.4 32.0 + - + +
110A VAL* 5.1 3.4 - - + -
168A GLU* 5.7 1.1 - - - -
170A LEU* 4.0 26.9 - - + -
173A ASP* 2.9 30.4 + - - -
174A VAL* 3.6 44.6 - - + -
177A THR* 3.1 23.2 + - - +
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Residues in contact with LEU 37 (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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36A TYR* 1.3 68.1 - - - +
38A VAL* 1.3 64.8 + - - +
105A PRO* 5.2 4.5 - - + -
106A ILE 3.8 16.4 - - - +
107A THR* 4.4 12.3 - - - +
120A ALA* 4.5 16.4 - - + +
166A CYS 4.7 1.2 - - - +
167A PRO 5.7 2.2 - - - -
168A GLU* 3.4 61.4 + - + +
169A GLY 4.9 0.3 + - - -
170A LEU* 5.3 2.8 + - - +
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Residues in contact with VAL 38 (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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36A TYR* 3.6 22.2 - - + +
37A LEU* 1.3 80.7 - - - +
39A ARG* 1.3 61.8 + - - +
105A PRO* 3.4 8.7 - - - +
106A ILE* 3.1 53.8 + - + +
108A LEU* 4.0 14.6 - - + -
164A LEU* 4.2 19.7 - - + -
165A GLU 3.7 12.8 - - - +
166A CYS 5.0 0.2 - - - -
167A PRO* 4.5 9.3 - - - +
170A LEU 4.3 16.2 - - - +
174A VAL* 4.8 7.9 - - + -
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Residues in contact with ARG 39 (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 VAL* 1.3 76.4 - - - +
40A TYR* 1.3 58.2 + - - +
41A MET* 3.3 27.5 + - - +
75A GLY 3.3 24.2 + - - -
76A ALA 2.9 19.3 + - - -
77A LYS* 3.6 9.3 - - - +
103A GLY* 3.6 21.6 + - - +
104A MET 3.3 20.2 - - - +
105A PRO* 4.2 1.8 - - + -
147A TYR* 4.7 0.4 + - - -
164A LEU* 3.0 8.3 - - - +
165A GLU* 2.9 47.6 + - + -
167A PRO* 2.9 38.7 - - + +
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Residues in contact with TYR 40 (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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39A ARG* 1.3 67.6 - - - +
41A MET* 1.3 68.2 + - - +
42A GLY* 3.7 27.7 + - - -
43A CYS* 4.0 10.3 - - + +
101A PHE* 5.4 12.8 - + + -
103A GLY 3.3 14.2 + - - -
104A MET* 2.9 27.9 + - + +
106A ILE* 3.9 28.8 - - + +
108A LEU* 6.2 0.4 - - + -
117A LEU* 3.7 29.2 - - + -
126A ILE* 5.2 11.9 - - + -
150A TYR* 5.4 1.6 - + - -
155A PRO* 5.1 3.1 - - - +
162A HIS* 3.1 40.4 + - + -
163A ILE 3.6 10.3 - - - -
164A LEU* 4.2 7.2 - - + -
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Residues in contact with MET 41 (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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39A ARG* 3.3 39.8 + - - +
40A TYR* 1.3 71.5 - - - +
42A GLY* 1.3 58.3 + - - +
69A VAL* 4.2 12.6 - - + +
70A CYS* 5.9 0.7 - - - -
73A VAL* 3.0 51.7 - - + +
76A ALA* 4.3 9.2 - - + -
102A ALA* 3.5 2.9 - - - -
103A GLY* 3.0 14.1 + - - +
147A TYR* 3.4 51.1 - - + +
163A ILE* 2.9 29.2 + - + +
164A LEU* 4.2 5.2 - - - -
165A GLU* 4.7 0.7 - - - -
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Residues in contact with GLY 42 (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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40A TYR* 3.2 21.5 - - - -
41A MET* 1.3 81.7 - - - +
43A CYS* 1.3 65.1 + - - +
69A VAL* 4.3 2.0 - - - -
99A LEU* 4.2 15.7 - - - -
101A PHE 4.9 2.5 - - - -
162A HIS* 3.6 2.3 - - - -
163A ILE* 3.0 29.5 + - - +
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Residues in contact with CYS 43 (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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40A TYR* 4.0 12.8 - - + +
42A GLY* 1.3 74.9 - - - +
44A VAL* 1.3 77.4 + - - +
69A VAL* 4.2 7.6 - - - +
97A SER* 3.9 2.8 - - - -
98A ASN* 3.3 35.3 + - - +
99A LEU* 3.9 13.7 - - + +
155A PRO* 4.1 25.8 - - + -
160A ALA* 4.3 1.3 - - - -
161A CYS 2.8 27.8 - - - -
162A HIS* 4.4 1.6 - - - -
163A ILE* 3.7 5.4 - - - +
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Residues in contact with VAL 44 (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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43A CYS* 1.3 79.1 - - - +
45A GLU* 1.3 56.7 + - - +
46A VAL* 3.5 18.2 - - + -
65A ALA* 3.5 35.2 - - + +
68A LEU* 4.8 2.0 - - + -
69A VAL* 3.5 27.8 - - + -
95A GLY* 4.0 1.6 - - - -
96A ARG* 2.9 37.9 - - - +
98A ASN* 4.1 4.9 - - - +
160A ALA* 3.5 2.4 - - - +
161A CYS* 3.1 36.1 + - + +
163A ILE* 4.2 3.1 - - + +
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Residues in contact with GLU 45 (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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44A VAL* 1.3 72.3 - - - +
46A VAL* 1.3 59.5 + - - +
95A GLY* 3.5 3.6 - - - -
96A ARG* 3.0 44.5 + - + +
97A SER 4.9 3.2 - - - +
98A ASN* 4.1 17.5 - - + +
156A VAL* 5.8 0.2 - - + -
158A GLN* 3.0 47.9 + - + +
159A ARG 3.4 13.2 - - - +
160A ALA* 4.3 2.0 - - + +
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Residues in contact with VAL 46 (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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44A VAL* 3.5 24.5 - - + +
45A GLU* 1.3 78.1 - - - +
47A LEU* 1.3 60.5 + - - +
48A GLN* 3.4 41.3 - - + +
49A SER 5.8 0.4 - - - +
61A VAL* 4.3 7.4 - - + -
65A ALA* 4.7 2.2 - - + -
94A LEU 4.0 2.9 - - - -
95A GLY* 4.7 2.0 - - - -
151A VAL* 5.0 4.3 - - + -
159A ARG* 3.1 46.5 + - + +
160A ALA* 3.9 7.0 - - - +
161A CYS* 3.7 12.3 - - + -
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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