Contacts of the strand formed by residues 3 - 9 (chain D) in PDB entry 2J3T
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 ILE 3 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ALA* 1.3 80.0 - - - +
4D PHE* 1.3 64.8 + - - +
5D SER 4.0 11.2 - - - +
6D VAL* 4.8 0.2 - - + -
21D SER* 3.1 31.2 - - - +
157D VAL* 4.0 13.0 - - + -
158D LEU 3.7 10.5 - - - +
159D ALA* 4.0 7.2 - - + -
163D GLN* 4.5 9.9 - - + +
166D ILE* 4.7 4.7 - - + -
169D LEU* 3.8 9.2 - - + -
206D LEU* 3.7 40.2 - - + +
209D ALA* 3.5 32.3 - - + -
210D GLU* 3.4 16.1 + - - +
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Residues in contact with PHE 4 (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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54C PRO* 3.5 35.0 - - + -
55C LEU* 4.9 11.9 - - + -
2D ALA* 4.6 14.6 - - + -
3D ILE* 1.3 77.7 - - - +
5D SER* 1.3 64.3 + - - +
21D SER* 2.8 24.2 + - - -
22D TYR* 3.2 31.1 - + + -
141D THR 3.5 22.4 - - - -
142D PHE* 3.9 4.0 - - + -
158D LEU* 2.8 19.7 + - + +
159D ALA* 3.5 19.7 - - - -
160D ASP* 3.4 31.9 - - + -
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Residues in contact with SER 5 (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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52C MET* 5.5 0.2 - - - +
3D ILE* 3.7 2.8 - - - +
4D PHE* 1.3 82.8 - - - +
6D VAL* 1.3 69.4 + - - +
7D TYR* 3.6 12.8 - - - -
19D LEU 3.1 13.7 - - - -
20D ASP* 3.5 15.3 - - - -
21D SER* 4.4 3.4 - - - -
22D TYR* 5.0 2.7 - - - -
157D VAL* 3.5 2.3 - - - +
158D LEU* 2.9 58.0 + - - +
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Residues in contact with VAL 6 (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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3D ILE* 4.8 1.1 - - + -
5D SER* 1.3 80.5 - - - +
7D TYR* 1.3 72.6 + - - +
8D VAL* 4.6 9.6 - - + -
17D TYR* 4.8 2.7 - - + -
18D GLN* 3.2 10.0 - - - +
19D LEU* 2.8 41.3 + - + +
21D SER* 5.8 0.2 - - - +
155D PHE* 5.9 0.7 - - - -
156D VAL 3.3 8.5 - - - +
157D VAL* 4.2 15.3 - - + -
173D ILE* 4.3 20.0 - - + -
202D LEU* 4.5 20.2 - - + -
206D LEU* 4.1 32.3 - - + -
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Residues in contact with TYR 7 (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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52C MET* 2.8 38.7 - - + +
5D SER* 3.6 24.0 - - - -
6D VAL* 1.3 80.2 - - - +
8D VAL* 1.3 62.6 + - - +
9D VAL* 4.0 5.4 - - + -
15D LEU* 4.2 20.0 - - + -
17D TYR 3.7 2.9 - - - -
18D GLN* 3.3 21.3 + - - -
20D ASP* 4.7 2.4 + - - -
103D LEU* 3.8 10.2 - - - +
108D LYS* 3.9 32.0 - - + +
111D LEU* 5.3 0.2 - - + -
112D ALA* 4.6 11.7 - - + -
154D LYS 3.4 1.9 - - - +
155D PHE* 3.6 1.0 - - - -
156D VAL* 2.6 61.7 + - + +
158D LEU* 4.5 7.4 - - + -
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Residues in contact with VAL 8 (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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6D VAL* 4.6 8.3 - - + -
7D TYR* 1.3 73.9 - - - +
9D VAL* 1.3 61.7 + - - +
15D LEU* 3.5 4.7 - - - +
16D ILE* 2.9 49.4 + - + +
17D TYR* 2.8 39.4 + - + -
153D ILE* 4.1 14.1 - - + -
154D LYS 3.3 6.1 - - - +
155D PHE* 3.9 22.9 - - + -
173D ILE* 4.9 2.7 - - + -
177D TYR* 5.1 0.7 - - + -
193D ILE* 4.1 9.2 - - + -
198D PHE* 4.5 11.9 - - + -
202D LEU* 5.8 0.2 - - + -
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Residues in contact with VAL 9 (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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7D TYR* 4.5 10.3 - - + +
8D VAL* 1.3 81.2 - - - +
10D ASN* 1.3 72.2 + - - +
13D GLY* 3.5 26.5 - - - +
14D GLY 3.4 10.1 - - - +
15D LEU* 5.0 0.9 - - + -
16D ILE* 4.8 1.1 - - - -
112D ALA* 4.1 28.5 - - + +
115D PHE* 5.3 5.4 - - + -
116D HIS* 5.1 3.4 - - + -
153D ILE* 3.6 9.0 - - - +
154D LYS* 2.9 49.5 + - + +
156D VAL* 4.5 13.5 - - + -
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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