Contacts of the strand formed by residues 99 - 106 (chain B) in PDB entry 3ZWG
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 THR 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B MET* 3.5 16.0 - - + +
91B ALA* 4.4 4.5 - - + -
92B TYR 3.5 2.7 - - - -
94B MET* 4.8 1.3 - - - -
98B ASN* 1.3 77.8 + - - +
100B LEU* 1.3 73.4 + - - +
101B ALA* 4.5 5.8 - - + +
120B ARG 3.8 0.2 - - - +
121B VAL* 3.4 8.1 - - - +
122B TYR* 2.8 48.0 + - + -
124B GLY 2.8 19.2 + - - -
125B GLN* 3.3 4.3 - - - -
126B LYS* 2.9 37.3 + - + +
132B MET* 4.9 1.8 - - + -
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Residues in contact with LEU 100 (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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37B ILE* 4.8 2.7 - - + -
45B TRP* 3.5 42.8 - - + -
90B ILE 3.6 0.7 - - - +
91B ALA* 3.4 4.3 - - - -
92B TYR* 2.9 43.5 + - + +
94B MET* 4.2 20.9 - - + +
99B THR* 1.3 73.7 - - - +
101B ALA* 1.3 63.5 + - - +
102B VAL* 4.6 17.2 - - + +
119B VAL* 4.1 11.7 - - + -
120B ARG 3.9 1.6 - - - +
121B VAL* 4.0 22.2 - - + +
154B LEU* 4.1 15.5 - - + -
158B LEU* 5.4 0.2 - - + -
176B VAL* 4.1 11.2 - - + -
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Residues in contact with ALA 101 (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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89B VAL* 4.4 0.2 - - + -
90B ILE 3.2 6.1 - - - +
91B ALA* 5.1 0.4 - - - -
99B THR* 4.6 3.1 - - + -
100B LEU* 1.3 75.5 - - - +
102B VAL* 1.3 65.5 + - - +
103B LEU 4.2 0.6 + - - -
118B ASN 3.9 0.3 - - - +
119B VAL* 3.5 2.8 - - - +
120B ARG* 3.0 37.4 + - - +
122B TYR* 3.9 16.4 - - + -
132B MET* 3.7 30.3 - - - -
136B LEU* 4.0 9.6 - - + +
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Residues in contact with VAL 102 (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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35B VAL* 5.3 0.9 - - + -
37B ILE* 4.0 24.0 - - + -
88B GLY 3.8 0.3 - - - +
89B VAL* 3.2 6.4 - - - -
90B ILE* 2.8 55.6 + - + +
100B LEU* 4.6 12.8 - - + -
101B ALA* 1.3 80.6 - - - +
103B LEU* 1.3 70.8 + - - +
104B PHE* 4.3 1.4 - - + -
118B ASN 3.3 9.0 - - - +
119B VAL* 4.2 18.2 - - + -
136B LEU* 4.6 0.2 - - - -
172B LEU* 4.4 6.5 - - + -
174B ILE* 3.6 24.0 - - + -
176B VAL* 6.2 0.2 - - + -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLY 3.3 12.8 - - - +
89B VAL* 4.4 3.6 - - + -
101B ALA 4.2 0.6 - - - -
102B VAL* 1.3 79.1 - - - +
104B PHE* 1.3 83.4 + - - +
105B SER* 4.2 4.9 - - - +
116B TRP* 5.2 1.6 - - + -
117B TRP* 3.2 11.9 - - - +
118B ASN* 2.9 48.2 + - + +
133B TYR* 4.2 27.4 - - + -
136B LEU* 3.5 45.3 - - + +
137B TYR* 3.8 13.5 - - + +
142B PRO* 4.2 7.9 - - + -
172B LEU* 4.4 0.2 - - - +
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Residues in contact with PHE 104 (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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33B ILE* 3.8 40.6 - - + -
35B VAL* 4.9 6.1 - - + -
50B THR* 4.5 2.9 - - + -
52B PHE* 3.9 19.7 - + - -
73B TYR* 5.2 5.2 - + - -
75B GLY* 5.7 0.9 - - - -
86B VAL* 3.9 31.0 - - + -
87B VAL* 3.2 0.9 - - - -
88B GLY* 2.7 75.0 + - - +
89B VAL 4.0 1.6 - - - -
90B ILE* 4.0 27.6 - - + -
102B VAL* 4.3 5.8 - - + -
103B LEU* 1.3 81.5 - - - +
105B SER* 1.3 59.3 + - - +
106B VAL* 5.2 0.2 - - + -
116B TRP 3.5 5.8 - - - +
117B TRP* 4.4 0.2 - - - +
164B MET* 4.8 0.7 - - + -
172B LEU* 4.2 11.0 - - + -
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Residues in contact with SER 105 (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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87B VAL* 3.2 23.8 - - - +
103B LEU* 4.2 1.8 - - - +
104B PHE* 1.3 74.8 - - - +
106B VAL* 1.3 61.9 + - - +
107B PRO* 3.6 10.1 - - - +
115B ASN* 3.4 7.8 - - - +
116B TRP* 2.8 40.5 + - - +
137B TYR* 3.6 36.0 + - - -
164B MET* 4.0 0.5 - - - +
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Residues in contact with VAL 106 (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 ARG* 4.2 8.1 - - - -
32B LYS 4.9 0.4 - - - +
33B ILE* 4.0 12.6 - - + -
85B GLY* 3.0 5.9 - - - -
86B VAL* 2.9 53.6 + - + +
87B VAL* 3.9 3.1 - - - +
105B SER* 1.3 76.5 + - - +
107B PRO* 1.3 61.7 - - - +
110B TYR* 3.6 11.9 - - - +
115B ASN* 3.3 11.4 - - - +
164B MET* 3.8 11.4 - - + -
167B SER 4.2 1.8 - - - +
168B GLY* 3.8 24.2 - - - +
170B ALA* 3.7 23.6 - - + -
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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