Contacts of the strand formed by residues 24 - 31 (chain B) in PDB entry 1XI1
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 VAL 24 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PHE* 3.9 26.5 - - + -
14B GLU 3.5 4.9 - - - +
15B THR* 3.5 11.7 - - + -
23B ARG* 1.3 77.3 + - - +
25B TRP* 1.3 62.4 + - - +
26B ALA 3.6 24.9 - - - +
27B TYR* 4.7 3.8 - - + -
42B ASN 4.4 6.9 - - - +
43B SER* 5.2 1.1 - - - +
44B LEU* 4.1 37.2 + - + +
69B PHE* 3.5 32.5 - - + -
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Residues in contact with TRP 25 (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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14B GLU* 2.7 54.9 + - + +
15B THR 3.4 27.8 + - - -
16B THR* 3.9 8.7 - - - +
23B ARG* 3.6 16.1 + - - +
24B VAL* 1.3 72.2 - - - +
26B ALA* 1.3 71.5 + - + +
42B ASN* 3.2 29.6 - - - +
146B ILE* 4.1 15.3 - - + -
148B TYR* 6.0 1.1 - + - -
152B ARG* 3.0 56.9 - - + +
156B TYR* 3.9 29.5 - + + +
158B ILE* 4.1 10.7 - - + +
162B GLU* 3.9 15.5 - - + -
166B ILE* 5.2 0.7 - - + -
5D T 5.0 0.6 - - - -
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Residues in contact with ALA 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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13B PHE* 3.4 3.1 - - - -
14B GLU* 2.8 33.5 + - + -
24B VAL* 3.5 7.3 - - - +
25B TRP* 1.3 98.4 - - + +
27B TYR* 1.3 61.3 + - - +
41B GLY 3.1 7.2 - - - -
42B ASN* 4.1 1.1 - - - +
158B ILE* 3.6 11.2 - - + -
166B ILE* 3.4 28.5 - - + -
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Residues in contact with TYR 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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12B ALA 3.3 7.6 - - - -
13B PHE* 3.8 24.7 - - + -
24B VAL* 4.7 3.8 - - + -
26B ALA* 1.3 75.6 - - - +
28B GLY* 1.3 65.4 + - - +
29B TYR* 4.2 13.2 - + - -
39B LYS* 3.8 28.3 - - - +
40B ILE* 3.3 11.3 - - - +
41B GLY* 2.8 64.7 + - - +
43B SER 3.5 29.4 - - - -
46B GLU* 2.7 28.4 + - - +
47B PHE* 3.8 34.7 + + + -
166B ILE* 4.2 6.3 - - - +
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Residues in contact with GLY 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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10B SER 3.9 0.2 - - - +
11B CYS* 3.2 6.2 - - - +
12B ALA 3.0 30.6 + - - -
27B TYR* 1.3 82.7 - - - +
29B TYR* 1.3 61.4 + - - -
39B LYS 3.0 13.2 - - - -
40B ILE* 4.2 7.4 - - - -
47B PHE* 5.1 0.9 - - - -
166B ILE* 4.3 8.2 - - - +
170B ILE* 4.0 8.4 - - - +
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Residues in contact with TYR 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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9B TYR* 3.7 15.9 - + + -
10B SER 3.4 6.5 - - - -
11B CYS* 3.8 13.5 - - - -
27B TYR* 4.2 17.9 - + - -
28B GLY* 1.3 74.2 - - - +
30B MET* 1.3 61.0 + - - +
37B GLU* 4.7 5.6 - - + -
38B TYR* 3.0 13.2 - - - +
39B LYS* 3.0 66.8 + - + +
47B PHE* 4.3 3.4 - + + -
50B TRP* 3.4 73.9 + + + -
170B ILE* 3.9 3.5 - - - +
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Residues in contact with MET 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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9B TYR* 3.1 6.8 - - - -
10B SER* 2.9 33.8 + - - +
29B TYR* 1.3 75.5 - - - +
31B ASN* 1.3 65.6 + - - +
32B ILE 3.0 5.5 + - - -
35B HIS* 3.9 29.4 - - - +
37B GLU 3.5 10.8 - - - +
38B TYR* 3.8 18.2 - - + -
167B LYS* 4.0 26.0 - - + +
170B ILE* 3.9 15.5 - - + +
171B GLN* 3.6 47.8 - - + +
174B ALA* 4.1 8.5 - - + -
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Residues in contact with ASN 31 (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 LYS* 4.0 17.5 - - - +
8B MET 3.4 14.5 + - - +
9B TYR* 3.6 11.8 - - + -
30B MET* 1.3 70.2 - - - +
32B ILE* 1.3 65.7 + - - +
33B GLU* 2.8 29.1 + - - +
34B ASP* 2.8 48.2 + - - +
35B HIS* 3.2 5.9 - - - -
37B GLU* 2.9 42.2 + - + +
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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