Contacts of the strand formed by residues 22 - 30 (chain B) in PDB entry 1P7Q
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 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B SER* 3.3 2.8 - - - -
12B ARG* 2.9 80.8 + - + +
13B HIS* 6.3 0.4 - + - -
21B ASN* 1.3 87.0 + - - +
23B LEU* 1.3 58.1 + - - +
24B ASN* 4.1 5.2 - - - +
50B GLU* 5.6 2.5 - - - -
67B TYR* 3.8 20.2 - + - -
68B THR* 3.0 22.4 - - - -
69B GLU* 3.8 34.3 - - + -
70B PHE* 3.0 12.4 - - - -
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Residues in contact with LEU 23 (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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9B VAL* 3.7 27.8 - - + -
10B TYR 3.9 7.2 - - - +
22B PHE* 1.3 70.1 - - - +
24B ASN* 1.3 70.8 + - - +
39B LEU* 3.5 24.0 - - + +
40B LEU 5.3 1.1 - - - +
46B ILE* 6.2 1.3 - - + -
66B TYR 3.5 1.0 - - - +
67B TYR* 3.0 23.4 - - - -
68B THR* 2.5 32.6 + - + +
70B PHE* 3.4 24.6 - - + -
78B TYR* 3.9 33.9 - - + -
79B ALA 4.8 9.2 - - - +
95B TRP* 4.8 5.6 - - + -
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Residues in contact with ASN 24 (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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236A ALA 3.0 27.5 + - - +
237A GLY* 5.0 0.7 - - - -
8B GLN 3.1 3.1 - - - +
9B VAL* 3.1 4.7 - - - +
10B TYR* 2.6 71.4 + - + +
12B ARG* 3.4 24.2 + - - +
22B PHE* 4.5 3.9 - - - +
23B LEU* 1.3 81.4 + - - +
25B CYS* 1.3 60.7 + - - +
65B LEU* 3.8 12.3 - - + +
66B TYR 3.4 1.6 - - - -
67B TYR* 3.0 27.3 - - - +
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Residues in contact with CYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.3 14.1 - - - -
8B GLN 3.4 2.5 - - - -
9B VAL* 4.5 0.9 - - - +
24B ASN* 1.3 74.0 - - - +
26B TYR* 1.3 61.4 + - - +
27B VAL* 3.9 6.4 + - - -
37B VAL* 4.1 12.3 - - + -
39B LEU* 3.6 13.9 - - + -
65B LEU* 3.2 4.8 - - - +
66B TYR* 2.9 33.0 + - - +
80B CYS* 2.0 50.9 - - + -
82B VAL* 4.2 8.5 - - - -
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Residues in contact with TYR 26 (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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232A GLU* 4.1 13.1 + - + -
233A THR 4.9 5.2 + - - -
234A ARG* 4.1 12.6 - - + -
235A PRO* 3.0 43.7 - - + +
6B LYS 2.7 22.2 - - - +
8B GLN* 2.9 28.4 + - + +
10B TYR* 3.4 27.4 - - + +
25B CYS* 1.3 72.0 - - - +
27B VAL* 1.3 51.7 + - - +
28B SER* 3.4 27.0 - - - -
63B TYR* 3.6 31.4 - + + +
64B LEU 3.1 28.3 - - - -
65B LEU* 4.1 2.9 - - + -
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Residues in contact with VAL 27 (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 PRO* 4.1 6.5 - - + -
6B LYS 3.2 3.6 - - - -
7B ILE* 4.3 13.7 - - + -
25B CYS* 3.9 6.3 + - - +
26B TYR* 1.3 71.9 - - - +
28B SER* 1.3 61.7 + - - +
30B PHE* 3.9 5.1 - - + -
35B ILE* 3.8 33.2 - - + -
37B VAL* 3.9 19.7 - - + -
63B TYR* 3.2 1.9 - - - -
64B LEU* 2.8 50.5 + - + +
66B TYR* 4.5 2.0 - - + -
82B VAL* 4.1 15.5 - - + -
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Residues in contact with SER 28 (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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232A GLU* 2.4 40.5 + - - -
5B PRO* 3.1 3.1 - - - +
6B LYS* 2.5 42.4 + - - +
26B TYR* 3.4 20.2 - - - -
27B VAL* 1.3 73.7 - - - +
29B GLY* 1.3 67.9 + - - +
30B PHE* 3.2 3.6 - - - -
62B PHE 3.5 5.8 - - - -
63B TYR* 3.8 10.5 - - - -
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Residues in contact with GLY 29 (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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232A GLU* 4.7 1.1 + - - -
3B ARG* 3.6 11.4 - - - +
4B THR 3.2 12.6 - - - +
6B LYS* 4.4 12.4 - - - +
28B SER* 1.3 76.3 - - - +
30B PHE* 1.3 56.3 + - - +
57B SER* 5.7 1.0 + - - -
61B SER* 3.0 32.4 + - - -
62B PHE 2.9 7.7 + - - -
63B TYR* 4.5 0.4 - - - +
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Residues in contact with PHE 30 (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 ARG* 3.3 11.9 - - - +
5B PRO* 3.1 27.4 - - + -
27B VAL* 3.9 10.3 - - + -
28B SER 4.1 6.3 - - - -
29B GLY* 1.3 78.2 - - - +
31B HIS* 1.3 62.1 + - - +
32B PRO 3.6 13.9 - - - -
33B SER* 3.2 24.7 - - - -
35B ILE* 3.2 40.2 - - + -
54B LEU* 4.8 1.3 - - + -
61B SER* 3.5 1.1 - - - -
62B PHE* 3.0 67.3 + - + -
63B TYR* 3.6 9.0 - - - -
64B LEU* 4.3 8.7 - - + -
84B HIS* 3.8 9.6 - + - -
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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