Contacts of the strand formed by residues 60 - 68 (chain B) in PDB entry 2B4J
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B SER* 3.5 36.4 + - - +
58B PRO 3.4 2.8 + - - -
59B GLY* 1.3 81.9 - - - +
61B TRP* 1.3 65.5 + - - +
78B HIS* 3.8 5.9 - - - -
79B VAL* 3.3 33.4 + - + +
111B LYS* 5.3 2.7 - - + -
112B THR* 3.6 28.9 - - + +
114B HIS* 3.2 40.2 - - + +
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Residues in contact with TRP 61 (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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58B PRO 4.6 1.0 + - - -
59B GLY 3.6 14.4 + - - -
60B ILE* 1.3 82.3 - - - +
62B GLN* 1.3 60.9 + - - +
63B LEU* 4.3 13.0 - - + -
76B ALA* 4.0 20.9 - - + -
77B VAL 3.2 8.5 - - - -
78B HIS* 3.5 39.0 - + + -
79B VAL* 4.2 3.1 - - - -
83B TYR* 3.6 26.9 - + - -
85B GLU* 5.0 0.9 - - + -
104B LEU* 3.8 18.2 - - + -
108B TRP* 3.5 44.4 - + + +
109B PRO* 4.6 3.0 + - + +
110B VAL* 3.7 31.2 - - + +
112B THR 2.9 9.9 + - - +
113B VAL* 3.3 7.3 - - + -
114B HIS* 2.8 27.2 + - - -
200B ILE* 3.8 12.1 - - + -
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Residues in contact with GLN 62 (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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61B TRP* 1.3 73.7 - - - +
63B LEU* 1.3 61.4 + - - +
75B VAL 3.7 0.7 - - - +
76B ALA* 3.4 1.7 - - - -
77B VAL* 2.7 45.2 + - + +
79B VAL* 4.0 16.5 - - + +
114B HIS* 3.4 29.7 - - + +
147B SER* 3.0 42.6 + - - +
148B GLN* 5.4 1.4 + - - -
150B VAL* 4.0 21.2 - - - +
151B ILE* 3.9 26.9 - - + +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TRP* 4.3 8.5 - - + -
62B GLN* 1.3 80.0 - - - +
64B ASP* 1.3 66.0 + - - +
74B LEU* 4.3 10.5 - - + -
75B VAL 3.1 11.9 - - - +
76B ALA* 3.8 19.5 - - + -
97B THR* 4.8 3.1 - - + -
100B PHE* 4.3 15.9 - - + -
101B LEU* 3.9 30.1 - - + -
104B LEU* 4.4 5.2 - - + -
113B VAL* 4.2 23.6 - - + -
114B HIS 3.0 15.3 + - - +
115B THR* 3.8 18.3 - - + -
116B ASP 4.6 1.2 + - - -
121B PHE* 4.0 19.4 - - + -
151B ILE* 4.2 1.7 - - - +
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Residues in contact with ASP 64 (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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63B LEU* 1.3 78.2 - - - +
65B CYS* 1.3 73.7 + - - +
74B LEU* 3.4 3.5 - - - +
75B VAL* 2.8 36.4 + - - +
116B ASP* 4.5 12.6 - - - +
121B PHE* 3.8 9.2 - - - -
148B GLN* 4.9 3.2 - - - +
151B ILE* 3.0 40.7 - - + +
152B GLU* 5.0 0.7 - - - +
155B ASN* 2.8 34.1 + - - +
302B PO4 4.9 0.5 + - - -
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Residues in contact with CYS 65 (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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64B ASP* 1.3 85.4 - - - +
66B THR* 1.3 61.6 + - - +
67B HIS* 4.3 6.6 - - + -
72B VAL* 4.1 13.5 - - + -
73B ILE 3.3 4.9 - - - +
74B LEU* 3.9 23.1 - - - -
89B ILE* 4.5 4.0 - - - -
92B GLU* 3.7 33.2 - - - +
116B ASP* 5.3 1.2 + - - -
120B ASN* 3.7 25.8 - - - -
121B PHE* 4.2 6.1 - - + -
302B PO4 4.3 4.5 + - - -
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Residues in contact with THR 66 (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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64B ASP* 4.1 1.0 + - - -
65B CYS* 1.3 75.5 - - - +
67B HIS* 1.3 68.6 + - - +
72B VAL* 3.8 0.9 - - - +
73B ILE* 2.8 52.4 + - + +
75B VAL* 4.2 8.1 - - + -
155B ASN* 3.6 27.5 + - + +
158B LEU* 5.1 3.6 - - + -
159B LYS* 2.9 35.7 + - + -
302B PO4 2.7 25.1 + - - -
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Residues in contact with HIS 67 (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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65B CYS* 4.3 8.3 - - + -
66B THR* 1.3 87.8 + - - +
68B LEU* 1.3 65.0 + - - +
70B GLY* 5.8 3.1 - - - +
71B LYS 3.2 9.9 - - - +
72B VAL* 3.9 18.8 - - + +
73B ILE* 4.8 0.4 - - - +
92B GLU* 2.7 36.2 + - - -
159B LYS* 3.2 21.6 + - - -
302B PO4 2.8 32.4 + - - +
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Residues in contact with LEU 68 (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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67B HIS* 1.3 78.5 - - - +
69B GLU* 1.3 71.3 + - + +
70B GLY 3.2 2.0 - - - -
71B LYS* 2.8 34.5 + - - +
73B ILE* 3.8 15.0 - - + +
159B LYS* 4.2 27.8 - - + +
162B ILE* 3.6 40.8 - - + -
172B LEU* 3.5 17.2 - - + +
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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