Contacts of the strand formed by residues 102 - 113 (chain A) in PDB entry 3GW5
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A THR* 4.8 7.6 - - + -
8A SER* 3.4 19.7 - - - +
97A ILE 4.0 0.4 - - - +
98A THR* 3.2 5.5 - - - -
99A VAL* 3.0 33.7 + - + +
101A GLY* 1.3 82.2 - - - +
103A THR* 1.3 68.9 + - - +
104A VAL* 4.7 1.1 - - + +
147A ILE* 3.8 32.3 - - + -
150A GLN* 4.1 19.5 - - - +
152A VAL* 4.3 10.1 - - + -
153A LEU* 3.8 28.9 - - + -
178A LEU* 4.0 15.5 - - + -
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Residues in contact with THR 103 (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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96A ILE* 3.3 33.2 - - + -
97A ILE 3.5 3.1 - - - -
98A THR* 3.1 21.0 - - + +
101A GLY 3.9 5.5 + - - -
102A ILE* 1.3 76.0 + - - +
104A VAL* 1.3 54.7 + - - +
150A GLN* 2.6 26.5 + - - +
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Residues in contact with VAL 104 (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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96A ILE* 4.4 3.6 - - - -
97A ILE* 2.8 46.9 + - + +
99A VAL* 5.8 0.9 - - + -
102A ILE* 5.0 1.3 - - + -
103A THR* 1.3 75.0 - - - +
105A THR* 1.3 68.0 + - - +
106A GLN* 3.4 3.9 + - + -
143A ILE* 3.7 34.3 - - + -
146A ASN* 3.4 38.8 - - + +
147A ILE* 4.2 15.0 - - + -
150A GLN* 3.6 12.3 - - + +
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Residues in contact with THR 105 (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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94A GLN* 3.5 38.8 - - + +
95A ASP 3.7 9.4 - - - +
96A ILE* 4.1 15.6 - - + +
104A VAL* 1.3 82.1 - - - +
106A GLN* 1.3 61.3 + - - +
146A ASN* 3.6 12.0 + - - -
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Residues in contact with GLN 106 (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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44A VAL* 4.4 11.6 - - + +
94A GLN* 3.5 5.1 - - - -
95A ASP 3.0 30.9 + - - +
97A ILE* 3.6 33.4 - - + -
104A VAL* 3.4 7.3 + - + +
105A THR* 1.3 75.3 - - - +
107A MET* 1.3 84.1 + - - +
108A PHE* 3.5 5.7 - - - -
140A VAL* 4.1 1.8 - - - +
141A THR 2.8 25.1 + - - -
142A PRO* 4.3 0.8 - - - +
143A ILE* 3.0 34.9 - - + +
146A ASN* 2.7 24.8 + - - +
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Residues in contact with MET 107 (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* 4.6 3.3 + - - +
73A LYS* 5.4 5.4 - - - +
75A ASN* 3.6 28.0 - - + +
92A LEU* 4.2 23.6 - - + -
93A SER 3.4 32.8 - - - +
94A GLN* 3.8 20.6 - - + +
106A GLN* 1.3 96.2 + - - +
108A PHE* 1.3 60.5 + - - +
140A VAL* 3.4 28.5 - - + +
146A ASN* 4.9 1.6 - - - +
1C NAG 4.2 9.4 - - - +
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Residues in contact with PHE 108 (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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26A ILE* 3.8 24.9 - - + -
44A VAL* 3.3 32.3 - - + +
45A TRP* 4.9 0.2 - - - -
46A VAL* 4.3 16.2 - - + -
64A PHE* 4.0 21.3 - + - -
92A LEU* 3.4 11.0 - - - -
93A SER* 2.9 52.2 + - - +
95A ASP* 3.6 26.7 - - + -
97A ILE* 4.3 10.5 - - + -
106A GLN 3.5 10.3 - - - -
107A MET* 1.3 74.7 - - - +
109A GLY* 1.3 72.7 + - - +
110A GLU* 4.1 20.0 - - + -
140A VAL* 5.4 0.2 - - - -
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Residues in contact with GLY 109 (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 2.7 17.1 + - - -
45A TRP* 3.2 9.1 - - - +
46A VAL 3.0 28.4 + - - +
79A LEU* 4.0 19.2 - - - +
90A GLY 6.1 0.2 - - - -
91A PHE 3.6 6.5 - - - -
92A LEU* 4.2 1.8 - - - +
108A PHE* 1.3 79.2 - - - +
110A GLU* 1.3 61.2 + - - -
111A VAL* 3.7 1.3 - - - -
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Residues in contact with GLU 110 (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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46A VAL 3.6 4.0 - - - +
48A SER* 2.6 33.3 + - - +
50A LYS* 4.2 5.4 - - - +
64A PHE* 3.6 36.5 - - + +
66A ALA* 3.9 7.1 + - - +
72A TYR* 3.8 9.9 + - - -
90A GLY* 3.2 3.5 - - - -
91A PHE* 2.9 58.7 + - + +
93A SER* 2.6 28.0 + - - +
108A PHE* 3.7 10.9 + - + -
109A GLY* 1.3 71.4 - - - -
111A VAL* 1.3 61.1 + - - +
112A THR 3.6 0.3 + - - -
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Residues in contact with VAL 111 (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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45A TRP* 3.2 44.4 - - + -
46A VAL 2.9 14.2 + - - +
47A PRO* 3.7 3.3 - - + +
48A SER* 2.8 26.9 + - - -
51A CYS* 3.5 7.0 - - - +
79A LEU* 6.3 1.3 - - + -
81A LEU* 5.8 0.7 - - + -
88A VAL* 3.9 19.1 - - + -
89A SER 3.5 10.1 - - - +
90A GLY* 4.3 0.4 - - - -
109A GLY* 4.8 1.3 - - - -
110A GLU* 1.3 72.3 - - - +
112A THR* 1.3 62.0 + - - +
113A GLU 3.3 28.5 - - - +
114A MET* 4.1 16.8 - - + -
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Residues in contact with THR 112 (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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48A SER* 4.1 3.8 - - - -
50A LYS* 4.0 24.5 - - + +
51A CYS* 3.2 28.8 - - - -
52A SER 4.2 1.0 + - - -
55A TYR* 3.4 8.7 - - - -
89A SER 2.8 3.5 + - - -
90A GLY* 3.5 14.0 + - - -
91A PHE* 3.9 30.2 - - + -
110A GLU 3.6 1.5 + - - +
111A VAL* 1.3 78.1 - - - +
113A GLU* 1.3 73.9 + - - +
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Residues in contact with GLU 113 (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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55A TYR* 3.4 27.7 + - + +
87A THR 4.2 0.4 - - - +
88A VAL* 3.3 9.0 - - - -
89A SER* 3.1 44.0 + - - +
111A VAL* 3.3 4.7 - - - +
112A THR* 1.3 93.2 + - - +
114A MET* 1.3 61.0 + - - +
115A PRO* 4.1 2.6 - - - +
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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