Contacts of the strand formed by residues 14 - 20 (chain B) in PDB entry 2P5G
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 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B GLN* 3.9 1.2 - - - -
11B ILE 2.9 36.5 + - - +
12B GLY 3.2 0.8 - - - -
13B ASP* 1.3 81.7 + - - +
15B ILE* 1.3 60.4 + - - +
16B PHE* 3.7 19.0 - - - -
30B GLU* 3.5 15.9 + - - -
31B VAL 3.3 4.0 - - - -
32B GLU* 2.7 27.3 + - - -
65B MSE 3.4 5.0 - - - +
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.7 23.8 - - + -
9B GLU 3.5 10.3 - - - +
10B GLN* 3.9 24.9 - - + -
14B SER* 1.3 70.7 - - - +
16B PHE* 1.3 66.3 + - - +
17B GLU* 4.3 1.1 - - + +
29B ARG 3.6 1.6 - - - +
30B GLU* 3.3 4.0 - - - -
31B VAL* 2.6 46.8 + - + +
33B TYR* 3.8 23.6 - - + -
65B MSE 3.8 9.6 - - + +
88B PHE 4.6 0.9 - - - +
89B LYS* 4.4 21.1 - - + +
92B TYR* 3.8 30.5 - - + -
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B THR 4.0 0.7 - - - +
8B VAL* 3.6 2.3 - - - +
9B GLU* 2.9 37.6 + - + +
11B ILE* 3.7 41.5 - - + -
14B SER* 3.7 23.6 - - - -
15B ILE* 1.3 71.3 - - - +
17B GLU* 1.3 60.3 + - - +
28B THR* 5.4 3.8 - - + -
29B ARG 3.6 2.9 - - - +
30B GLU* 3.2 40.2 - - + -
245B HIS* 3.7 51.3 - + + +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 3.3 10.1 - - + +
7B THR 3.5 9.9 - - - +
8B VAL* 4.5 4.7 - - + +
15B ILE* 3.9 3.3 + - + -
16B PHE* 1.3 74.5 - - - +
18B ARG* 1.3 68.8 + - - +
19B TYR* 3.7 7.1 - - - +
27B ARG 3.9 0.5 - - - +
28B THR* 3.3 7.2 - - - +
29B ARG* 2.4 70.8 + - + +
31B VAL* 5.8 0.2 - - + -
92B TYR* 2.5 37.9 + - + +
97B TYR* 2.4 37.0 + - - -
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 3.9 0.3 - - - -
6B LEU* 2.6 40.4 + - + +
7B THR* 2.9 33.6 + - - +
16B PHE 4.3 0.2 - - - -
17B GLU* 1.3 73.6 - - - +
19B TYR* 1.3 53.5 + - - +
26B GLU* 2.9 33.2 + - - +
27B ARG 3.6 4.9 - - - +
28B THR* 3.8 14.4 + - - +
209B THR* 2.9 44.3 + - - +
210B PRO 2.7 25.9 + - - -
211B VAL* 3.6 13.0 - - - +
244B PRO* 4.1 15.2 - - + +
245B HIS* 4.0 12.6 - - - +
267B GLY 3.2 17.3 + - - -
268B ILE* 4.2 0.2 - - - +
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU* 3.8 21.0 + - - -
4B PHE 3.6 12.6 - - - +
5B TYR* 3.7 8.5 - - - -
6B LEU* 3.9 5.8 - - - +
17B GLU* 3.7 5.6 - - - +
18B ARG* 1.3 76.1 - - - +
20B ILE* 1.3 80.3 + - - +
21B ASP* 4.0 12.9 - - + +
26B GLU* 3.4 8.0 - - - +
27B ARG* 2.9 71.2 + - + +
28B THR 5.5 0.2 - - - -
29B ARG* 3.3 64.1 + - + +
97B TYR* 3.7 8.3 - - - +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MSE 3.9 4.9 - - - -
3B GLU* 3.6 2.4 - - - -
4B PHE* 3.0 69.0 + - + +
6B LEU* 3.8 20.0 - - + -
19B TYR* 1.3 89.1 - - - +
21B ASP* 1.3 72.7 + - - +
24B GLY* 3.6 23.3 - - - +
25B ARG 3.6 2.0 - - - -
26B GLU* 3.8 21.5 - - + +
107B LYS* 3.8 24.9 - - + +
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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