Contacts of the strand formed by residues 94 - 103 (chain C) in PDB entry 3VA2
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 PHE 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ILE* 3.9 20.4 - - + -
46C VAL* 4.1 9.2 - - + -
48C LEU* 3.9 18.2 - - + -
69C ILE* 3.6 35.0 - - + -
71C ALA* 3.2 18.2 - - - -
72C PRO* 4.0 5.4 - - + -
86C CYS* 4.0 18.2 - - + -
88C THR* 3.6 31.0 - - + -
89C ILE 4.9 0.2 - - - -
90C LEU* 4.3 14.1 - - + -
93C GLY* 1.3 74.3 - - - +
95C SER* 1.3 59.7 + - - +
96C ALA* 3.7 20.4 - - + -
117C GLU* 3.2 4.2 - - - +
118C LEU* 2.6 49.1 + - + +
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Residues in contact with SER 95 (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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69C ILE* 3.6 3.1 - - - +
70C ASN* 2.8 46.8 + - - +
71C ALA* 3.1 23.5 + - - +
94C PHE* 1.3 77.1 - - - +
96C ALA* 1.3 64.2 + - - +
115C SER* 5.9 1.7 - - - -
116C ALA 3.7 8.1 + - - -
117C GLU* 4.1 15.4 + - - +
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Residues in contact with ALA 96 (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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36C PHE* 3.6 6.0 - - + -
38C ILE* 4.2 7.4 - - + -
48C LEU* 4.0 22.0 - - + -
68C LYS 3.2 10.8 - - - +
69C ILE* 4.3 3.8 - - + -
70C ASN* 3.7 2.5 + - - +
94C PHE* 3.7 23.0 - - + -
95C SER* 1.3 77.2 + - - +
97C SER* 1.3 67.2 + - - +
115C SER* 3.5 1.2 - - - -
116C ALA 3.0 32.7 + - - +
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Residues in contact with SER 97 (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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36C PHE* 4.2 2.9 - - - -
67C VAL* 3.5 4.5 - - - +
68C LYS* 2.6 45.4 + - - +
70C ASN* 3.1 20.0 + - - -
96C ALA* 1.3 73.5 + - - +
98C VAL* 1.3 61.7 - - - +
113C TRP* 3.4 25.9 - - - +
114C ALA 3.3 6.3 - - - -
115C SER* 2.7 25.0 + - - -
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Residues in contact with VAL 98 (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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33C PRO* 3.7 24.2 - - + +
36C PHE* 3.7 34.1 - - + -
50C TRP* 4.0 32.8 - - + -
65C TYR* 4.2 5.6 - - + -
66C GLN 3.3 9.9 - - - +
67C VAL* 4.5 4.7 - - + -
97C SER* 1.3 76.2 - - - +
99C ARG* 1.3 72.9 + - - +
113C TRP* 3.6 4.4 - - - -
114C ALA* 2.8 42.3 + - + +
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Residues in contact with ARG 99 (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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33C PRO* 4.0 2.5 - - - -
65C TYR* 3.3 15.9 - - - +
66C GLN* 2.8 65.0 + - + +
98C VAL* 1.3 76.3 - - - +
100C THR* 1.3 64.5 + - - +
101C ILE* 4.4 0.2 - - + -
108C LEU* 6.3 0.2 - - - +
110C ALA* 3.8 23.0 - - - +
111C SER* 3.4 27.8 + - - +
112C SER 4.2 1.8 - - - +
113C TRP* 3.2 51.2 - - + +
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Residues in contact with THR 100 (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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30C LEU* 3.2 16.6 - - + +
31C LEU 3.0 20.7 + - - +
33C PRO* 3.2 17.5 - - - +
63C LEU* 3.8 32.5 - - + -
64C GLU 3.6 10.1 - - - +
65C TYR* 4.0 11.6 - - + -
99C ARG* 1.3 74.6 - - - +
101C ILE* 1.3 64.1 + - - +
110C ALA* 3.4 2.8 - - - -
111C SER* 2.9 40.6 + - - -
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Residues in contact with ILE 101 (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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30C LEU* 4.0 1.3 - - - -
62C ASN 4.9 0.2 - - - +
63C LEU* 4.0 4.7 - - - +
64C GLU* 2.8 60.5 + - + +
65C TYR 3.6 15.9 - - - +
66C GLN* 3.8 29.8 - - + +
78C GLU* 3.8 31.4 - - + +
99C ARG* 4.1 4.0 - - + -
100C THR* 1.3 79.6 - - - +
102C LEU* 1.3 62.8 + - - +
103C GLN* 3.9 15.7 - - + +
108C LEU* 5.6 8.5 - - + -
109C LEU 3.3 8.3 - - - +
110C ALA* 4.5 7.0 - - + -
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Residues in contact with LEU 102 (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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28C ILE* 3.6 43.1 - - + -
30C LEU* 3.7 13.9 - - + +
61C VAL* 3.6 31.4 - - + -
62C ASN 4.1 7.2 - - - +
63C LEU* 3.8 20.2 - - + -
101C ILE* 1.3 74.2 - - - +
103C GLN* 1.3 65.8 + - - +
104C ASN* 6.1 2.7 - - - +
107C SER 4.1 0.9 - - - +
108C LEU* 3.5 0.7 - - - -
109C LEU* 2.6 53.2 + - + +
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Residues in contact with GLN 103 (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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109A ARG* 3.9 2.8 - - - +
64C GLU* 3.5 24.6 + - - +
78C GLU* 3.5 23.4 + - - +
101C ILE* 3.9 11.0 - - + +
102C LEU* 1.3 86.2 - - - +
104C ASN* 1.3 67.0 + - - +
107C SER 3.6 7.0 - - - +
108C LEU* 3.3 32.3 - - + +
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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