Contacts of the strand formed by residues 66 - 70 (chain B) in PDB entry 2P7I
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 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.3 24.2 - - + -
47B GLU* 4.7 2.2 - - + -
56B THR* 4.1 5.6 - - + -
59B LEU* 3.8 15.9 - - + +
60B GLN* 3.7 42.8 - - + +
63B PHE* 3.7 25.4 - - + +
65B ASP* 1.3 79.4 + - - +
67B THR* 1.3 67.9 + - - +
68B CYS* 3.9 23.1 - - - -
86B GLY 3.2 6.2 + - - +
87B ILE* 3.2 16.0 - - + -
88B THR* 2.8 24.9 + - - -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU 2.9 6.8 + - - -
46B LEU* 3.4 16.7 - - + +
47B GLU* 2.7 32.1 + - - -
66B ILE* 1.3 76.6 + - - +
68B CYS* 1.3 59.4 + - - +
88B THR* 3.3 19.7 - - + +
90B ILE* 3.5 31.6 - - + -
100B PRO* 5.5 0.7 - - + -
101B ARG* 3.7 13.5 + - - -
103B TYR* 3.5 32.4 + - - +
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Residues in contact with CYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU* 3.5 15.7 - - - -
50B SER* 3.3 18.2 - - - +
56B THR* 3.6 27.8 - - - -
66B ILE* 3.9 9.0 - - - -
67B THR* 1.3 73.3 - - - +
69B VAL* 1.3 58.3 + - - +
70B GLU 4.1 0.3 + - - -
76B ILE* 4.7 2.0 - - + +
83B LEU* 5.3 0.4 - - - -
87B ILE* 3.5 25.6 - - + -
88B THR 2.7 12.5 + - - +
89B TYR* 3.5 13.2 - - + +
90B ILE* 2.8 32.4 + - - +
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Residues in contact with VAL 69 (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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46B LEU* 3.9 23.6 - - + -
47B GLU 3.0 6.1 + - - -
48B LEU* 3.9 15.7 - - + -
49B GLY 2.8 31.4 + - - -
50B SER* 3.2 4.4 + - - -
68B CYS* 1.3 73.7 - - - +
70B GLU* 1.3 64.0 + - - +
90B ILE* 3.3 26.7 - - + +
92B SER 3.7 19.1 - - - +
94B PHE* 3.8 20.1 - - + -
97B ALA* 4.5 9.9 - - + -
99B LEU* 4.1 14.1 - - + -
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Residues in contact with GLU 70 (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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49B GLY* 3.6 8.2 - - - -
50B SER* 3.5 17.5 + - - +
51B PHE* 2.8 50.5 + - - +
68B CYS 4.1 0.2 + - - -
69B VAL* 1.3 75.8 - - - +
71B ALA* 1.3 64.7 + - - +
72B SER* 3.0 42.1 + - - +
75B ALA* 4.2 1.3 - - + -
76B ILE* 3.8 15.3 - - + +
90B ILE 3.1 5.9 + - - -
91B HIS* 3.3 12.1 - - - -
92B SER 3.1 20.8 + - - -
94B PHE* 5.5 0.9 - - - -
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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