Contacts of the strand formed by residues 96 - 102 (chain A) in PDB entry 3NBV
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 SER 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A VAL* 4.0 4.0 - - - -
14A LEU* 3.1 31.2 - - - +
16A VAL* 5.2 1.1 - - - -
68A VAL* 5.9 1.1 - - - -
94A THR 3.6 4.1 + - - -
95A PRO* 1.3 76.9 - - - +
97A SER* 1.3 63.9 + - - +
112A LEU* 3.6 1.7 - - - +
113A HIS* 2.8 36.8 + - - +
115A THR* 4.9 0.4 - - - +
35B GLN* 3.0 21.9 + - - -
37B TRP* 4.4 11.8 + - - -
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU 2.9 5.3 + - - -
15A ASP* 2.7 27.8 + - - -
16A VAL* 3.0 28.4 + - - +
96A SER* 1.3 77.7 + - - +
98A CYS* 1.3 64.4 + - - +
99A CYS* 3.1 12.0 - - - -
110A ILE* 4.2 6.1 - - - -
111A VAL 3.1 17.9 - - - -
112A LEU* 4.0 8.3 - - - -
300A FRU 4.0 9.9 - - - -
35B GLN* 4.1 5.4 - - - -
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Residues in contact with CYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.4 11.2 - - - +
97A SER* 1.3 77.6 - - - +
99A CYS* 1.3 61.3 + - - +
100A ILE* 4.1 1.5 + - + +
109A THR 3.6 1.2 - - - +
110A ILE* 3.5 1.9 - - - -
111A VAL* 2.8 48.2 + - + +
16B VAL* 3.3 37.5 - - - -
18B SER* 4.3 6.1 - - - +
35B GLN* 3.9 6.7 + - - -
98B CYS* 3.7 33.2 - - + -
100B ILE* 6.0 0.4 - - + -
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Residues in contact with CYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP* 3.7 24.7 - - - -
16A VAL 2.9 7.3 + - - +
17A ILE* 3.4 16.7 - - + +
18A SER* 2.9 28.2 + - - +
97A SER* 3.1 24.2 - - - -
98A CYS* 1.3 76.2 - - - +
100A ILE* 1.3 64.6 + - - +
101A ILE* 3.9 3.7 + - + -
108A ARG* 5.8 1.1 - - + -
109A THR 3.2 7.2 - - - +
110A ILE* 4.0 21.5 - - + -
254A LEU* 4.3 12.6 - - + -
300A FRU 4.5 0.7 - - - -
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 3.6 8.1 - - - +
20A VAL* 3.7 31.9 - - + -
23A TYR* 4.1 30.0 - - + +
24A PRO* 4.7 7.6 - - + -
98A CYS* 4.1 1.8 - - + -
99A CYS* 1.3 76.7 - - - +
101A ILE* 1.3 63.9 + - - +
102A ASN 4.0 1.0 + - - +
107A ASN 3.8 0.3 - - - +
108A ARG* 3.2 3.3 - - - -
109A THR* 2.8 47.7 + - + +
23B TYR* 5.8 0.4 - - - +
98B CYS* 4.9 10.3 - - - -
100B ILE* 4.3 23.1 - - + -
109B THR* 6.5 0.2 - - + -
111B VAL* 3.8 26.5 - - + -
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Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.8 18.2 - - + -
18A SER 2.9 12.0 + - - +
19A LEU* 3.3 15.2 - - + +
20A VAL* 2.9 31.0 + - - +
36A ARG* 3.6 17.5 - - - +
99A CYS* 4.8 2.9 - - + +
100A ILE* 1.3 77.2 - - - +
102A ASN* 1.3 62.0 + - - +
103A ASN 3.3 0.9 + - - -
106A GLY 4.6 1.3 - - - +
107A ASN 3.4 8.1 - - - +
108A ARG* 4.2 10.3 - - + -
251A VAL 3.5 25.6 - - - +
252A ASP* 3.1 35.2 - - + +
254A LEU* 4.1 15.9 - - + -
292A GLN* 4.3 1.6 - - - +
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Residues in contact with ASN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.5 9.4 - - + +
21A ASP 3.5 8.8 - - - +
22A LYS* 4.4 1.8 - - - +
23A TYR* 3.9 21.5 - - + +
100A ILE* 4.0 1.8 + - - +
101A ILE* 1.3 68.2 - - - +
103A ASN* 1.3 56.7 + - - +
104A SER* 2.8 28.0 + - - -
105A ASN* 3.3 25.6 + - - +
106A GLY* 2.8 34.5 + - - -
107A ASN* 2.8 13.9 + - + +
251A VAL 4.0 0.2 - - - +
26B GLU* 2.7 29.4 + - + +
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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