Contacts of the strand formed by residues 58 - 65 (chain B) in PDB entry 2GOO
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 HIS 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.7 6.5 - - - +
38B CYS* 4.2 0.9 - - - -
55B THR* 3.9 2.6 - - - +
57B GLY* 1.3 79.7 - - - -
59B CYS* 1.3 66.0 + - - +
77B CYS* 3.5 3.1 - - - -
78B MET* 2.8 42.4 + - + +
80B TYR* 4.0 13.5 - + - -
83B SER* 3.1 39.5 + - - -
87B CYS* 4.3 9.4 - - - -
101B CYS* 4.1 15.9 - - + +
102B CYS* 3.5 9.7 + - - +
103B ARG* 3.2 36.5 + - + +
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Residues in contact with CYS 59 (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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36B LEU* 3.9 10.1 - - - -
37B LYS 3.4 12.1 - - - -
38B CYS* 2.1 43.5 - - - -
58B HIS* 1.3 73.7 - - - +
60B PHE* 1.3 62.5 + - - +
76B GLY 3.3 5.8 - - - -
101B CYS* 3.1 5.5 - - - +
102B CYS* 2.9 29.8 + - - -
104B THR 4.0 3.1 - - - -
106B LEU 4.4 0.7 - - - -
107B CYS* 3.8 26.9 - - - -
108B ASN* 3.7 18.6 - - - +
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Residues in contact with PHE 60 (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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50A PRO* 3.6 29.4 - - + -
52A ALA* 4.7 5.2 - - + -
43B HIS* 3.8 32.1 - + + -
59B CYS* 1.3 75.8 - - - +
61B ALA* 1.3 68.5 + - - +
62B ILE* 4.1 7.2 - - + -
75B SER* 3.1 5.0 - - - -
76B GLY* 2.8 67.9 + - - -
77B CYS 3.5 21.5 - - - -
78B MET* 4.0 15.3 - - + -
99B ILE* 4.1 17.5 - - + -
100B GLU 3.1 12.3 - - - +
101B CYS* 4.2 8.1 - - - -
108B ASN* 2.6 21.0 - - - +
111B LEU* 4.8 0.9 - - - -
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Residues in contact with ALA 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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60B PHE* 1.3 77.6 - - - +
62B ILE* 1.3 61.8 + - - +
73B LEU* 4.3 2.9 - - + -
74B ALA 3.4 9.2 - - - +
75B SER* 4.4 3.8 - - - -
99B ILE* 3.4 3.3 - - - +
100B GLU 2.9 30.7 + - - -
108B ASN* 3.7 4.5 + - - +
111B LEU* 3.6 42.8 - - + +
113B PRO* 3.7 12.7 - - + +
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Residues in contact with ILE 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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49A PHE* 3.8 38.8 - - + +
50A PRO* 4.0 8.7 - - + -
43B HIS* 4.3 7.2 - - - +
60B PHE* 4.1 14.4 - - + -
61B ALA* 1.3 77.1 - - - +
63B ILE* 1.3 72.0 + - - +
64B GLU* 4.2 16.5 + - - +
72B THR 3.7 0.9 - - - +
73B LEU* 3.4 7.5 - - - +
74B ALA* 2.8 55.7 + - + +
97B ARG* 4.2 14.8 - - + -
98B THR 3.3 11.7 - - - +
99B ILE* 4.0 11.9 - - + -
113B PRO* 4.8 0.2 - - - -
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Residues in contact with ILE 63 (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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62B ILE* 1.3 73.8 - - - +
64B GLU* 1.3 62.4 + - - +
71B THR* 4.3 13.5 - - - +
72B THR 3.4 12.3 - - - +
73B LEU* 4.6 10.3 - - + +
97B ARG* 3.0 5.0 - - - +
98B THR* 2.8 46.3 + - - +
112B GLN* 6.0 0.9 - - + -
113B PRO* 3.3 39.2 - - + +
114B THR* 4.0 1.6 - - - -
115B LEU* 3.7 45.3 - - + +
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Residues in contact with GLU 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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49A PHE 4.5 10.4 - - - +
43B HIS* 5.0 4.5 + - - -
62B ILE* 4.4 27.6 - - + +
63B ILE* 1.3 76.7 - - - +
65B GLU* 1.3 62.6 - - - +
66B ASP 3.9 1.6 + - - +
70B GLU 4.0 0.3 - - - +
71B THR* 3.2 3.9 - - - -
72B THR* 3.0 48.2 + - - +
74B ALA* 5.1 4.9 - - - +
95B LEU* 6.1 4.2 - - + +
96B ARG 3.6 4.9 - - - +
97B ARG* 3.7 20.7 + - + -
115B LEU* 4.1 2.9 - - - -
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Residues in contact with GLU 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 GLU* 1.3 72.9 - - - +
66B ASP* 1.3 73.8 + - - +
69B GLY* 3.7 29.5 - - - +
70B GLU 4.1 3.1 - - - -
71B THR* 4.0 14.2 - - + +
95B LEU* 3.8 17.4 - - - +
96B ARG* 2.4 75.4 + - + +
115B LEU* 3.9 6.4 - - + +
118B VAL* 5.4 0.7 - - - +
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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