Contacts of the strand formed by residues 86 - 94 (chain C) 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 VAL 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C ARG 4.6 2.2 - - - +
32C LYS* 4.5 17.5 - - - +
33C ILE* 4.4 10.3 - - + -
52C PHE* 4.1 9.2 - - + -
54C SER 3.2 9.4 - - - +
75C GLY 4.0 14.4 - - - -
76C GLN 3.9 23.1 - - - +
77C LYS 4.2 0.2 - - - +
85C GLY* 1.3 73.9 - - - +
87C VAL* 1.3 63.4 + - - +
104C PHE* 3.8 21.1 - - + -
105C SER* 3.9 0.7 - - - -
106C VAL* 2.9 49.4 + - + +
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C PHE* 3.6 2.2 - - - -
53C ARG* 2.8 39.1 + - + -
54C SER* 2.8 23.7 + - - +
85C GLY* 4.8 2.0 - - - +
86C VAL* 1.3 81.6 - - - +
88C GLY* 1.3 61.1 + - - +
103C LEU* 4.9 0.2 - - + -
104C PHE* 3.2 11.0 - - - +
105C SER* 3.2 27.6 - - - +
106C VAL 3.9 9.0 - - - +
107C PRO* 5.3 2.0 - - + -
133C TYR* 3.4 36.3 - - + +
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TYR* 3.1 13.0 - - - -
52C PHE* 4.4 1.1 - - - -
53C ARG* 4.3 1.8 - - - -
87C VAL* 1.3 78.2 - - - +
89C VAL* 1.3 69.4 + - - +
103C LEU* 3.3 3.4 - - - +
104C PHE* 2.7 56.1 + - - +
133C TYR* 5.4 0.9 - - - -
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C THR* 3.2 4.7 - - - +
51C TYR* 2.8 40.0 + - + +
88C GLY* 1.3 80.6 - - - +
90C ILE* 1.3 74.5 + - - +
102C VAL 3.1 9.6 - - - +
103C LEU* 4.4 7.0 - - + -
104C PHE* 4.0 1.4 - - - -
128C ALA* 3.6 13.8 - - + +
132C MET* 3.8 27.4 - - - -
133C TYR* 3.8 36.6 - - + +
136C LEU* 3.8 18.2 - - + -
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Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C VAL* 4.5 17.9 - - + -
37C ILE* 4.9 12.6 - - + -
49C ASN 3.6 3.1 - - - -
50C THR* 3.9 14.1 - - + +
61C LEU* 4.0 11.7 - - + -
71C LEU* 5.7 1.3 - - + -
73C TYR* 4.0 24.0 - - + -
89C VAL* 1.3 79.1 - - - +
91C ALA* 1.3 64.7 + - - +
92C TYR* 3.8 31.6 - - + -
100C LEU 3.6 0.5 - - - +
101C ALA* 3.2 6.2 - - - -
102C VAL* 2.8 41.3 + - + +
104C PHE* 4.0 23.6 - - + -
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ALA* 4.3 0.3 - - - -
48C MET* 2.9 40.4 + - + +
49C ASN* 2.9 22.0 + - - +
61C LEU* 4.4 1.0 - - - +
90C ILE* 1.3 77.2 - - - +
92C TYR* 1.3 64.1 + - - +
99C THR* 4.4 4.7 - - + -
100C LEU 3.4 4.7 - - - -
126C LYS 4.0 5.2 - - - +
128C ALA* 3.9 26.5 - - + +
132C MET* 5.1 3.1 - - - -
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Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ILE* 5.4 2.9 - - + -
45C TRP* 3.9 26.5 - + + -
46C THR 3.4 11.7 - - - +
47C ALA* 3.3 27.1 - - + -
48C MET* 3.6 3.1 - - - -
61C LEU* 3.7 11.5 - - + +
62C PRO* 2.8 49.9 + - - +
63C HIS 4.4 1.6 - - - -
65C VAL* 4.0 11.4 - - + -
71C LEU* 3.4 31.2 - - + +
90C ILE* 3.8 28.7 - - + -
91C ALA* 1.3 73.5 - - - +
93C SER* 1.3 60.1 + - - +
99C THR* 3.5 2.8 - - - +
100C LEU* 2.9 44.4 + - + +
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Residues in contact with SER 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C THR 3.9 0.5 - - - +
45C TRP* 3.3 4.2 - - - +
46C THR* 2.7 53.5 + - - -
48C MET* 3.5 23.0 - - - +
92C TYR* 1.3 73.2 - - - +
94C MET* 1.3 65.9 + - - +
98C ASN 3.5 8.3 - - - -
125C GLN* 4.2 25.0 + - - -
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Residues in contact with MET 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LYS* 4.4 9.2 - - + -
44C THR 3.6 4.7 - - - -
45C TRP* 3.7 27.4 - - + +
92C TYR 4.5 0.2 - - - +
93C SER* 1.3 82.0 + - - +
95C SER* 1.3 59.9 + - - +
96C ASP* 2.9 40.4 + - - +
97C GLY* 3.1 14.2 + - - -
98C ASN* 2.8 27.2 + - + +
99C THR 4.5 0.4 - - - +
100C LEU* 4.1 27.6 - - + +
121C VAL* 4.1 14.8 - - + -
125C GLN* 5.9 0.9 + - - -
156C TYR* 5.4 0.9 - - + -
158C LEU* 3.8 30.7 - - + -
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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