Contacts of the strand formed by residues 86 - 99 (chain C) in PDB entry 2V10
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 GLY 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C TYR* 3.1 38.1 + - - +
85C THR* 1.4 73.1 - - - +
87C THR* 1.3 64.7 + - - -
115C PRO* 5.9 0.7 - - - -
117C LEU 5.5 0.2 - - - -
118C PRO* 4.3 15.0 - - - -
119C PHE* 4.4 7.6 - - - -
1341C C61 5.7 0.2 - - - -
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Residues in contact with THR 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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80C THR* 3.6 24.5 - - + -
81C LEU 3.0 15.3 - - - +
82C ARG* 3.9 18.4 - - + +
83C TYR 4.6 0.7 + - - -
86C GLY* 1.3 73.6 + - - -
88C VAL* 1.3 67.5 + - - +
89C SER* 5.6 1.1 - - - +
115C PRO* 2.9 33.2 - - - +
119C PHE* 4.0 0.5 - - - -
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TRP* 3.9 19.3 - - + +
80C THR* 3.8 1.9 - - - +
81C LEU* 2.9 50.0 + - + +
83C TYR* 4.3 3.1 - - + -
87C THR* 1.3 76.9 - - - +
89C SER* 1.3 59.5 + - - +
111C VAL* 3.8 20.6 - - + -
113C GLU* 3.4 13.5 - - - +
114C MET* 4.9 3.4 - - + -
115C PRO* 4.3 2.2 - - + -
119C PHE* 3.2 42.8 - - + -
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Residues in contact with SER 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU* 6.0 0.7 - - - +
79C LEU 3.6 4.2 + - - -
80C THR* 2.6 31.2 + - - +
81C LEU* 6.0 0.4 - - - -
87C THR* 5.6 1.3 - - - -
88C VAL* 1.3 74.6 - - - +
90C GLY* 1.3 59.5 + - - +
111C VAL* 3.2 23.8 - - - +
112C THR* 3.2 7.0 + - - -
113C GLU* 3.0 37.2 + - - +
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Residues in contact with GLY 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU* 3.4 12.7 + - - +
79C LEU* 2.9 30.9 + - - -
89C SER* 1.3 78.7 + - - +
91C PHE* 1.3 65.5 + - - +
110C GLU 3.4 10.8 - - - -
111C VAL* 3.9 3.1 - - - -
112C THR* 3.9 12.6 - - - -
113C GLU* 5.0 1.0 + - - -
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Residues in contact with PHE 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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48C SER* 4.4 1.6 - - - -
50C LYS* 3.6 35.7 - - + -
72C TYR* 5.1 6.5 - - - -
74C HIS* 5.4 5.8 - + - -
76C GLY* 3.9 20.4 - - - +
77C THR 3.2 13.0 - - - +
78C GLU* 4.3 7.4 - - - +
79C LEU* 4.6 2.4 - - - +
90C GLY* 1.3 76.1 - - - +
92C LEU* 1.3 82.1 + - - +
93C SER* 4.4 2.9 - - - -
109C GLY* 3.3 1.5 - - - -
110C GLU* 2.9 70.5 + - + +
112C THR* 4.1 16.6 - - + -
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Residues in contact with LEU 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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43C ASN* 5.6 1.6 - - - +
75C ASN* 3.9 14.4 - - + +
76C GLY 3.0 19.8 + - - +
77C THR* 2.8 37.9 + - - +
78C GLU 5.3 0.4 - - - +
79C LEU* 3.1 38.4 - - + -
91C PHE* 1.3 79.0 - - - +
93C SER* 1.3 68.9 + - - +
107C MET* 4.9 11.4 - - - -
108C PHE* 3.1 20.6 - - - +
138C GLY* 5.7 2.7 - - - -
140C VAL* 4.0 26.7 - - + -
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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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72C TYR* 3.5 23.5 - - - -
73C LYS 3.7 4.7 - - - -
75C ASN* 4.4 7.6 - - - +
91C PHE* 4.6 2.2 - - - -
92C LEU* 1.3 79.4 + - - +
94C GLN* 1.4 62.6 + - - +
107C MET* 3.2 10.1 - - - +
108C PHE* 2.7 48.6 + - - -
110C GLU* 2.8 29.3 + - - +
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Residues in contact with GLN 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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72C TYR* 3.2 1.5 - - - -
73C LYS* 2.6 81.1 + - + +
93C SER* 1.4 70.5 - - - +
95C ASP* 1.3 63.7 - - - +
105C THR* 3.6 36.2 + - - +
106C GLN 3.3 11.9 - - - +
107C MET* 3.2 35.7 - - + +
108C PHE* 4.1 1.3 - - - -
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Residues in contact with ASP 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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26C ILE* 4.1 5.6 - - + -
27C GLY* 3.3 12.2 - - - -
64C PHE* 3.7 6.6 - - + -
69C SER* 2.6 25.2 + - - -
71C SER* 2.6 29.9 + - - -
72C TYR* 2.9 25.5 - - + +
94C GLN* 1.3 78.3 - - - +
96C ILE* 1.3 72.7 + - - +
97C ILE* 4.6 1.2 - - - +
105C THR* 3.4 4.7 - - - -
106C GLN* 3.1 25.7 + - - +
108C PHE* 3.7 19.1 - - + -
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Residues in contact with ILE 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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25C GLY 3.7 0.6 - - - +
26C ILE* 3.4 2.1 - - - -
27C GLY* 3.0 25.4 + - - +
28C THR* 3.1 33.2 - - + +
71C SER* 4.6 9.0 - - - +
95C ASP* 1.3 82.1 + - - +
97C ILE* 1.3 60.6 + - - +
98C THR* 5.1 6.7 - - - +
103C THR* 4.4 17.9 - - + -
104C VAL 3.2 10.1 - - - +
105C THR* 3.0 27.6 - - + +
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Residues in contact with ILE 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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24C ILE* 3.9 22.9 - - + -
25C GLY 3.4 4.0 - - - +
26C ILE* 3.3 31.6 - - + -
44C VAL* 3.9 20.0 - - + -
95C ASP 3.8 2.2 + - - +
96C ILE* 1.3 79.2 - - - +
98C THR* 1.3 72.0 + - - +
99C VAL* 4.4 0.7 - - + -
103C THR* 3.5 2.6 - - - +
104C VAL* 2.6 39.6 + - + +
105C THR* 4.5 0.2 - - - +
106C GLN* 3.7 28.9 - - + -
108C PHE* 4.0 9.9 - - + -
143C ILE* 4.1 16.4 - - + -
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Residues in contact with THR 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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23C GLU 4.6 0.2 - - - +
24C ILE* 3.5 8.1 - - - +
25C GLY* 2.9 37.5 + - - -
30C PRO* 5.6 4.9 - - - +
96C ILE* 4.9 7.1 + - - +
97C ILE* 1.3 78.2 - - - +
99C VAL* 1.3 61.0 + - - +
100C GLY 3.9 1.3 + - - -
101C GLY* 4.6 13.5 - - - +
102C ILE 3.5 9.2 - - - +
103C THR* 3.2 24.5 + - - +
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Residues in contact with VAL 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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10C VAL* 4.9 5.8 - - + -
23C GLU 5.2 0.2 - - - -
24C ILE* 3.6 26.0 - - + -
37C PHE* 4.4 14.8 - - + -
97C ILE* 4.4 1.3 - - + -
98C THR* 1.3 72.4 - - - +
100C GLY* 1.3 65.3 + - - +
101C GLY 3.4 0.2 - - - -
102C ILE* 2.9 26.3 + - + +
104C VAL* 5.3 2.9 - - + -
128C VAL* 5.4 2.0 - - + -
143C ILE* 3.9 27.1 - - + -
147C ILE* 3.8 29.4 - - + -
178C LEU* 4.6 12.5 - - + +
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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