Contacts of the strand formed by residues 13 - 20 (chain C) in PDB entry 2V16
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 GLN 13 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C THR 3.8 1.9 - - - +
9C TYR* 2.8 51.0 + - + +
11C ASP 3.5 1.0 - - - -
12C THR* 1.2 86.4 - - - +
14C TYR* 1.3 57.9 + - - +
15C TYR* 4.0 9.7 - - + -
114C LEU 3.2 17.0 - - - +
115C ALA* 3.4 1.9 - - - -
116C GLU* 3.1 49.4 + - - +
117C PHE* 4.0 9.5 - - + -
1327C C47 3.4 38.9 - - + -
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Residues in contact with TYR 14 (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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6C LEU* 4.5 11.5 - - + +
7C THR 3.4 7.4 - - - -
8C ASN* 3.5 20.4 + - + -
11C ASP* 3.7 25.3 + - - -
13C GLN* 1.3 73.6 - - - +
15C TYR* 1.3 57.6 + - - +
30C VAL* 3.9 20.7 - - - +
31C PHE* 4.7 1.9 + - - -
155C TYR* 3.3 67.6 + + + +
156C ASN 2.5 27.5 + - - -
162C GLY 3.4 26.2 - - - -
303C ALA* 3.9 9.9 - - + -
307C ARG* 3.4 20.8 + - - -
1327C C47 3.9 9.4 + - - -
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Residues in contact with TYR 15 (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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6C LEU* 3.0 5.8 - - - -
7C THR* 2.7 67.1 + - + +
9C TYR* 4.2 6.6 - - + +
13C GLN* 4.0 20.9 - - + -
14C TYR* 1.3 73.4 - - - +
16C GLY* 1.4 59.4 + - - +
17C GLU* 5.9 0.7 - - + -
28C LYS* 3.6 39.3 - - + -
29C VAL 3.2 24.9 - - - +
30C VAL* 4.0 0.7 - - + +
31C PHE* 5.5 0.2 - - - -
116C GLU* 3.4 38.5 + - + -
117C PHE* 3.9 22.7 - + + -
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Residues in contact with GLY 16 (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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4C VAL* 4.2 1.3 - - - -
5C ILE 3.8 9.4 - - - -
6C LEU* 3.7 10.5 - - - -
15C TYR* 1.4 58.7 - - - +
17C GLU* 1.3 59.4 + - - -
28C LYS* 3.5 4.2 - - - +
29C VAL* 2.7 36.0 + - - +
31C PHE* 3.7 19.1 - - - -
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Residues in contact with GLU 17 (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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4C VAL* 4.0 19.6 - - + +
5C ILE 4.9 1.1 + - - +
15C TYR* 5.9 0.9 - - + -
16C GLY* 1.3 75.8 - - - +
18C ILE* 1.2 76.3 + - - +
26C THR* 4.2 22.9 - - + +
27C PHE 3.7 7.4 - - - +
28C LYS* 3.5 29.8 + - + +
31C PHE* 4.5 0.4 - - - -
90C THR 4.3 2.6 - - - +
91C VAL* 4.8 0.2 - - - -
92C GLY 4.8 6.1 + - - -
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Residues in contact with ILE 18 (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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17C GLU* 1.2 87.5 - - - +
19C GLY* 1.4 56.3 - - - +
20C ILE* 3.7 28.0 - - + -
26C THR* 3.8 5.6 + - - -
27C PHE* 2.9 38.9 + - + +
29C VAL* 4.0 15.3 - - + -
31C PHE* 3.9 19.7 - - + -
38C VAL* 5.1 3.8 - - + -
40C VAL* 5.2 2.7 - - + -
89C ILE* 4.0 13.5 - - + -
90C THR 3.4 9.9 - - - +
91C VAL* 3.8 27.4 - - + -
121C VAL* 4.2 17.0 - - + -
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Residues in contact with GLY 19 (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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18C ILE* 1.4 71.4 - - - +
20C ILE* 1.3 65.4 + - - -
21C GLY 3.9 0.2 + - - -
24C PRO* 4.6 9.6 - - - +
25C GLN 3.7 10.5 - - - -
26C THR* 4.3 5.8 - - - -
88C ILE 3.7 0.7 - - - +
89C ILE* 3.4 1.7 - - - -
90C THR* 3.0 45.5 + - - -
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Residues in contact with ILE 20 (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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18C ILE* 3.7 21.3 - - + -
19C GLY* 1.3 72.6 - - - -
21C GLY* 1.3 70.6 + - - +
23C PRO 4.0 0.7 - - - +
25C GLN* 3.0 28.8 + - - +
27C PHE* 3.7 25.6 - - + -
38C VAL* 5.6 0.7 - - + -
40C VAL* 4.7 13.0 - - + -
56C PHE* 3.5 23.0 - - + -
87C ASP* 3.9 4.9 - - + -
88C ILE 3.4 9.6 - - - +
89C ILE* 3.4 28.5 - - + -
101C PHE* 3.5 30.5 - - + -
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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