Contacts of the strand formed by residues 79 - 91 (chain B) in PDB entry 2X5Q
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 TYR 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B VAL* 4.0 17.5 - - + -
58B LEU 3.1 14.6 - - - +
59B THR* 3.9 11.2 - - + -
61B TYR 3.2 9.0 + - - -
76B PRO 5.7 0.9 - - - -
77B CYS 3.7 12.3 - - - -
78B ASP* 1.3 74.4 - - - +
80B VAL* 1.3 58.8 + - - +
81B LYS* 3.4 25.3 + - + -
142B PHE* 3.5 14.6 - - - -
186B ASN* 2.9 42.0 + - - -
187B TYR* 4.1 2.9 - - - -
188B TYR* 2.8 51.3 + + - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.6 5.7 - - + -
14B PRO* 4.0 15.7 - - + -
15B ILE 5.2 0.9 - - - +
16B THR* 5.3 1.1 - - + -
58B LEU* 2.9 35.5 + - + +
61B TYR 3.7 3.4 - - - +
62B ALA* 3.6 10.5 - - - -
63B ILE* 3.6 35.2 - - + +
70B LEU* 3.9 26.2 - - + -
79B TYR* 1.3 80.1 - - - +
81B LYS* 1.3 74.8 + - - +
187B TYR* 4.0 13.9 - - + -
188B TYR 3.9 3.8 - - - +
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.7 2.5 - - - -
14B PRO* 3.9 0.7 - - - +
15B ILE 3.3 21.0 + - - +
55B ILE* 4.2 2.9 - - + -
56B LEU 3.3 5.2 - - - +
57B VAL* 4.1 27.1 - - + -
79B TYR* 3.4 23.1 + - + -
80B VAL* 1.3 84.1 - - - +
82B GLY* 1.3 59.6 + - - +
108B ILE* 4.9 5.9 - - + +
183B GLU 5.1 0.6 + - - -
184B ILE* 2.8 38.4 + - + +
185B PHE* 3.8 19.9 - - + -
186B ASN* 3.1 38.2 + - - +
187B TYR* 4.4 1.4 - - - +
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Residues in contact with GLY 82 (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 PHE* 3.4 13.6 - - - -
13B LEU 3.3 13.2 - - - -
15B ILE* 4.3 0.9 - - - -
55B ILE* 3.3 7.8 - - - +
56B LEU* 2.9 34.1 + - - -
81B LYS* 1.3 78.1 - - - +
83B ILE* 1.3 65.9 + - - -
185B PHE* 3.7 7.9 - - - -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL 3.4 1.6 - - - +
12B PHE* 3.6 2.5 - - - -
13B LEU* 2.8 53.0 + - + +
15B ILE* 4.6 7.2 - - + -
45B SER* 3.3 19.7 - - - +
52B LEU* 4.5 14.6 - - + -
55B ILE* 4.8 2.7 - - + -
82B GLY* 1.3 78.3 - - - +
84B LEU* 1.3 61.4 + - - +
85B ILE* 3.7 22.4 - - + -
157B VAL* 5.7 0.2 - - + -
158B LEU* 4.2 16.6 - - + -
161B ILE* 4.0 20.4 - - + -
162B TYR* 4.1 7.9 - - + +
185B PHE* 3.9 20.6 - - + -
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Residues in contact with LEU 84 (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 GLN* 3.3 8.5 - - + +
11B VAL 3.4 2.9 - - - +
12B PHE* 3.9 17.7 - - + -
44B VAL* 3.3 34.8 + - + -
45B SER* 2.8 30.5 + - - -
54B ASN 5.2 2.7 - - - +
56B LEU* 4.1 31.0 - - + -
82B GLY 4.3 0.2 + - - -
83B ILE* 1.3 73.8 - - - +
85B ILE* 1.3 64.5 + - - +
105B LEU* 4.8 9.4 - - + -
107B ILE* 4.9 5.2 - - + -
117B ILE* 4.7 15.5 - - + -
119B PHE* 3.8 37.5 - - + -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN* 3.1 9.2 + - - -
11B VAL* 2.8 48.7 + - + +
13B LEU* 3.7 31.4 - - + -
35B ILE* 4.4 2.9 - - + -
37B TYR* 3.5 31.2 - - + -
43B HIS* 3.4 17.0 - - + +
83B ILE* 3.7 16.2 - - + -
84B LEU* 1.3 79.5 - - - +
86B SER* 1.3 61.7 + - - +
87B GLY 3.4 0.2 + - - -
161B ILE* 4.1 11.2 - - + -
162B TYR* 3.4 21.3 - - - +
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Residues in contact with SER 86 (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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8B GLU* 3.0 33.4 + - - +
9B GLU 3.6 10.9 + - - -
10B GLN* 3.5 7.6 + - - +
37B TYR* 3.5 6.2 - - - +
38B ASN* 2.9 37.1 + - - -
41B GLY* 3.7 9.6 - - - -
42B GLN 3.6 12.3 - - - -
43B HIS* 2.9 18.3 + - - -
85B ILE* 1.3 70.1 - - - +
87B GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 87 (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 GLU* 3.8 11.4 + - - +
10B GLN 4.6 0.2 - - - -
11B VAL* 3.3 19.1 - - - +
36B GLU* 3.0 14.8 - - - -
37B TYR* 4.0 2.0 - - - -
38B ASN* 3.4 18.7 + - - +
85B ILE 3.4 3.4 + - - -
86B SER* 1.3 75.0 + - - +
88B LYS* 1.3 68.4 + - - +
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Residues in contact with LYS 88 (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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11B VAL* 3.8 8.9 - - - +
35B ILE* 3.4 4.0 - - - -
36B GLU* 2.8 50.7 + - + +
38B ASN* 5.8 2.9 - - - +
87B GLY* 1.3 77.6 - - - +
89B ILE* 1.3 64.4 + - - +
90B LEU* 3.2 8.4 + - + +
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Residues in contact with ILE 89 (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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11B VAL* 3.9 15.0 - - + +
33B VAL* 4.7 2.0 - - + -
34B SER 3.8 5.8 - - - +
35B ILE* 4.4 13.0 - - + -
88B LYS* 1.3 71.5 - - - +
90B LEU* 1.3 61.6 + - - +
91B LYS 3.3 22.7 - - - +
92B GLY* 3.7 20.3 - - - +
93B ASN 4.2 2.0 - - - +
94B HIS* 3.5 36.3 + - + +
120B SER* 4.0 14.8 - - - +
121B LEU 3.6 26.9 - - - -
122B PRO* 3.6 12.6 - - + -
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Residues in contact with LEU 90 (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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26B GLN* 3.4 38.8 - - + +
34B SER 2.9 11.9 + - - +
35B ILE 4.6 0.2 - - - -
36B GLU* 3.4 46.4 - - + +
88B LYS* 3.2 10.9 + - + +
89B ILE* 1.3 73.5 - - - +
91B LYS* 1.3 60.7 + - + +
92B GLY 5.3 0.2 - - - -
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Residues in contact with LYS 91 (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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30B GLY 5.4 0.4 - - - -
31B SER 3.1 27.9 + - - -
32B SER* 3.4 14.3 - - - +
33B VAL* 3.2 18.1 - - - +
34B SER* 3.2 30.5 + - - +
89B ILE* 3.3 11.9 - - - +
90B LEU* 1.3 81.0 - - + +
92B GLY* 1.3 64.1 + - - +
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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