Contacts of the strand formed by residues 15 - 21 (chain A) in PDB entry 2VF8
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 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PHE* 4.5 12.3 - - + -
11A PRO 3.6 22.2 - - - -
12A ASP* 4.4 3.6 - - + -
13A GLY* 3.2 12.1 - - - -
14A GLY* 1.3 85.6 - - - +
16A VAL* 1.3 66.7 + - - +
17A GLN* 4.3 5.7 + - + +
32A LYS* 3.1 52.3 - - + -
33A VAL 3.6 5.2 - - - -
34A PRO* 3.5 31.0 - - + -
35A ARG* 2.9 22.2 + - - -
89A ASP 4.3 0.7 - - - +
90A GLY* 4.1 4.0 - - - -
449A TRP* 3.6 31.9 - + - -
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Residues in contact with VAL 16 (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 PHE* 1.3 74.7 - - - +
17A GLN* 1.3 63.9 + - - +
18A VAL* 4.0 7.3 - - + +
31A VAL 3.7 1.0 - - - +
32A LYS* 3.3 7.3 - - - +
33A VAL* 2.8 42.5 + - + +
35A ARG* 3.6 16.4 - - + +
57A LEU* 4.6 5.8 - - + -
88A ILE* 3.9 20.6 - - + -
89A ASP 3.3 12.3 - - - +
90A GLY 3.4 19.1 - - - +
91A LEU* 4.1 10.8 - - + -
92A PRO* 4.6 6.1 - - + -
435A PHE* 4.6 15.3 - - + -
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Residues in contact with GLN 17 (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 PHE* 4.1 5.2 - - + +
16A VAL* 1.3 72.2 - - - +
18A VAL* 1.3 64.0 + - - +
19A ARG* 3.8 28.1 + - - +
30A SER* 6.0 1.0 - - - -
31A VAL 3.4 11.7 + - - -
32A LYS* 3.1 38.1 - - - +
87A ALA 3.6 0.5 - - - +
88A ILE* 3.0 5.3 - - - -
89A ASP* 2.6 56.4 + - + +
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Residues in contact with VAL 18 (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* 4.6 5.4 - - + +
17A GLN* 1.3 79.4 + - - +
19A ARG* 1.3 66.6 + - - +
21A ALA* 4.1 26.2 - - + +
29A ILE 4.9 0.9 - - - +
30A SER* 3.3 5.9 - - - -
31A VAL* 2.9 52.3 + - + +
33A VAL* 5.7 4.0 - - + -
52A LEU* 4.8 2.7 - - + -
56A THR* 4.6 3.6 - - + -
57A LEU* 3.4 30.7 - - + -
85A VAL* 4.4 1.8 - - + -
87A ALA 3.4 8.1 - - - +
88A ILE* 3.8 15.9 - - + -
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Residues in contact with ARG 19 (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 GLN* 3.8 23.0 + - + +
18A VAL* 1.3 74.6 - - - +
20A GLY* 1.3 65.2 + - - +
21A ALA 3.6 1.8 - - - -
30A SER* 3.3 20.2 - - - +
85A VAL* 3.9 1.2 - - - +
86A ASP* 3.2 7.8 + - + +
87A ALA* 2.8 50.8 + - + +
89A ASP* 2.5 31.7 + - - -
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Residues in contact with GLY 20 (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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19A ARG* 1.3 73.0 - - - +
21A ALA* 1.3 57.8 + - - -
22A ARG* 3.1 12.3 + - - -
28A ASP* 3.5 21.3 - - - -
29A ILE 2.9 16.0 + - - -
30A SER* 3.5 4.4 + - - -
85A VAL* 3.2 3.5 - - - -
86A ASP* 3.0 31.3 + - - -
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Residues in contact with ALA 21 (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 VAL* 4.1 19.3 - - + -
19A ARG 3.6 0.4 - - - -
20A GLY* 1.3 75.1 - - - +
22A ARG* 1.3 59.7 + - - +
23A GLN 3.9 0.2 - - - -
26A LEU* 3.8 9.4 - - + +
28A ASP* 3.0 22.0 + - - -
29A ILE* 3.0 33.4 + - + +
52A LEU* 4.9 2.0 - - + -
56A THR* 4.2 21.8 - - + +
84A ASP 3.8 4.9 - - - -
85A VAL* 4.1 2.7 - - + -
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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