Contacts of the strand formed by residues 103 - 113 (chain D) in PDB entry 2VSC
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 ARG 103 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C PCA 3.7 16.4 + - + +
2C LEU* 3.4 21.1 - - + +
27C ASN* 2.7 50.5 + - - +
29C GLU* 3.3 33.6 + - - +
99C THR* 3.4 5.2 - - - +
100C GLU* 2.9 60.0 + - + +
31D GLN* 6.1 0.2 - - - +
35D GLU* 3.0 42.6 + - + +
101D LEU 3.6 4.5 + - - +
102D THR* 1.3 77.7 - - - +
104D GLU* 1.3 62.6 + - - +
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C PCA 3.2 13.9 + - - +
2C LEU* 3.1 23.5 + - - -
97C GLU* 4.4 17.0 - - + +
98C VAL 3.3 13.2 - - - +
99C THR* 4.1 12.1 + - + +
102D THR* 5.5 2.7 - - + -
103D ARG* 1.3 74.8 - - - +
105D GLY* 1.3 59.6 + - - +
106D GLU* 4.6 8.6 - - - +
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Residues in contact with GLY 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C PCA 4.9 1.1 - - - -
2C LEU* 3.7 10.3 - - - +
4C PHE* 3.4 18.6 - - - -
97C GLU* 3.5 4.3 - - - +
98C VAL 3.1 28.4 + - - +
104D GLU* 1.3 79.3 - - - +
106D GLU* 1.3 65.0 + - - +
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Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C PHE* 3.2 12.8 - - - -
6C LYS* 5.7 2.6 - - - -
95C THR* 3.9 22.4 - - + +
96C CYS 3.0 14.1 - - - +
97C GLU* 4.0 20.9 - - - +
104D GLU* 4.6 7.4 - - - +
105D GLY* 1.3 75.1 - - - +
107D THR* 1.3 61.7 - - - +
108D ILE* 5.7 5.4 - - + +
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Residues in contact with THR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C PHE* 3.6 33.1 - - + +
5C ASN 6.1 0.2 - - - +
6C LYS* 3.5 33.5 - - - +
7C THR 5.2 1.1 + - - +
23C CYS* 4.0 19.3 - - + -
24C PHE 5.6 0.2 - - - +
95C THR* 3.3 4.2 - - - +
96C CYS 2.8 31.6 + - - -
106D GLU* 1.3 75.4 - - - +
108D ILE* 1.3 70.6 + - - +
109D ILE* 4.1 15.1 - - + +
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Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LYS* 6.1 0.2 - - - +
7C THR 3.4 13.0 + - - +
8C LYS* 4.3 4.5 - - - +
93C ASN* 3.4 34.5 - - + +
94C TYR 3.1 6.1 - - - +
95C THR* 3.7 26.2 - - + +
1119C NAG 3.7 28.4 + - - +
106D GLU* 5.7 5.4 - - + +
107D THR* 1.3 84.7 + - - +
109D ILE* 1.3 65.0 + - - +
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C THR* 3.6 19.5 - - + +
8C LYS 3.7 2.7 - - - -
9C SER 4.1 2.7 - - - -
10C VAL* 4.1 18.6 - - + +
21C ILE* 3.6 17.4 - - + +
22C PRO* 3.4 34.5 - - + +
40C TRP* 3.7 26.7 - - + -
93C ASN* 3.8 3.1 - - - -
94C TYR* 2.8 39.2 + - - +
107D THR* 4.1 20.6 - - + +
108D ILE* 1.3 80.1 - - - +
110D GLU* 1.3 71.1 + - - +
111D LEU 3.8 0.3 + - - -
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Residues in contact with GLU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS* 3.0 22.5 + - - +
9C SER* 3.2 6.0 - - - -
10C VAL 2.8 30.3 + - - +
92C GLY* 3.5 15.0 - - - +
93C ASN* 3.2 18.0 + - - +
1119C NAG 3.3 36.7 + - + +
109D ILE* 1.3 74.4 - - - +
111D LEU* 1.3 67.4 + - - +
112D LYS* 3.3 33.7 - - + +
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Residues in contact with LEU 111 (chain D).
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* 3.5 24.7 - - + +
12C PHE* 3.7 38.1 - - + -
19C VAL* 3.8 18.4 - - + -
21C ILE* 4.4 8.1 - - + -
82C MET* 5.5 0.2 - - - -
87C ALA* 4.0 16.8 - - + +
90C HIS 3.7 20.9 - - - +
91C THR* 3.6 6.4 - - + -
92C GLY* 2.9 27.5 + - - +
94C TYR* 3.8 26.0 - - + +
1116C NAG 3.8 3.6 - - + -
109D ILE 3.8 1.8 + - - -
110D GLU* 1.3 74.1 - - - +
112D LYS* 1.3 62.4 + - - +
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Residues in contact with LYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS* 5.0 10.6 - - - +
9C SER* 3.9 25.2 + - - +
10C VAL 2.8 12.4 + - - +
11C GLU* 3.1 24.1 - - + +
12C PHE* 2.9 31.9 + - - -
91C THR* 4.6 1.3 - - - -
110D GLU* 3.3 40.6 + - + +
111D LEU* 1.3 78.4 - - - +
113D TYR* 1.3 59.7 + - - +
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLU* 4.5 3.4 - - - +
12C PHE* 3.3 36.3 - + + -
13C THR* 3.6 22.9 - - - -
14C PHE* 3.6 32.0 + + - +
84C LYS* 6.2 0.4 - - + -
88C VAL* 4.9 15.0 - - + +
91C THR* 3.9 22.6 - - + +
112D LYS* 1.3 73.9 - - - +
114D ARG* 1.3 71.5 + - - +
115D VAL* 3.8 25.4 + - + +
116D VAL 5.5 0.3 + - - -
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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