Contacts of the strand formed by residues 82 - 87 (chain B) in PDB entry 1EFP
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 ARG 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B LYS* 5.2 4.4 - - - +
57B GLU* 3.1 34.0 + - - +
58B ILE 3.3 3.4 + - - +
59B ILE* 3.6 28.1 - - + +
60B ALA* 3.0 24.4 + - - +
76B LEU* 3.4 11.7 - - - +
80B ALA* 3.5 0.5 - - - +
81B ASP* 1.3 83.4 - - + +
83B ALA* 1.3 63.7 + - - +
84B ILE* 4.0 10.5 - - - +
112B GLU* 2.9 35.1 + - - +
202B PRO* 3.9 23.1 - - + +
204B ASP* 3.9 21.8 + - - -
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Residues in contact with ALA 83 (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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59B ILE* 4.9 0.4 - - - -
60B ALA* 3.0 13.9 - - + +
72B LEU* 3.6 30.3 - - + -
76B LEU* 4.0 13.9 - - + -
82B ARG* 1.3 78.3 - - - +
84B ILE* 1.3 64.0 + - - +
202B PRO 3.2 10.2 + - - +
203B LEU* 3.3 8.2 - - + -
204B ASP* 3.0 30.8 + - - +
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Residues in contact with ILE 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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59B ILE* 4.0 16.2 - - + -
60B ALA 2.9 5.9 + - - -
61B VAL* 3.2 14.0 - - + +
62B SER 3.1 23.0 + - - -
72B LEU* 3.5 4.7 - - - +
82B ARG* 4.0 11.9 - - - +
83B ALA* 1.3 80.1 - - - +
85B LEU* 1.3 62.4 + - - +
86B VAL* 4.4 13.9 - - + -
108B VAL* 4.0 12.6 - - + -
112B GLU* 3.9 36.3 - - + +
204B ASP* 3.5 20.0 - - + +
206B LYS* 4.8 6.7 - - + -
211B TYR* 3.9 19.7 - - - +
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Residues in contact with LEU 85 (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 SER 3.4 13.7 - - - +
63B ILE 5.0 0.2 - - - +
64B GLY 5.0 1.1 - - - +
65B VAL 4.0 4.5 - - - +
66B LYS* 3.7 20.9 - - - +
68B ALA* 3.3 31.6 - - + -
69B ALA* 4.1 12.6 - - + +
72B LEU* 3.5 17.2 - - + +
84B ILE* 1.3 73.6 - - - +
86B VAL* 1.3 61.1 + - - +
87B VAL* 4.0 21.1 - - + -
203B LEU* 4.0 11.6 - - + +
204B ASP 2.9 10.0 + - - +
205B GLU* 3.6 18.5 - - + +
206B LYS 2.7 34.1 + - - +
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Residues in contact with VAL 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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61B VAL* 4.4 13.0 - - + -
62B SER 3.0 8.5 + - - -
63B ILE* 3.2 19.9 - - + +
64B GLY 3.0 24.1 + - - -
84B ILE* 4.4 6.7 - - + -
85B LEU* 1.3 72.4 - - - +
87B VAL* 1.3 60.4 + - - +
104B ILE* 3.9 28.7 - - + -
108B VAL* 4.6 1.3 - - + -
206B LYS* 3.7 3.1 - - + -
207B THR 3.6 7.9 - - - +
208B ALA* 3.6 32.1 - - + +
211B TYR* 3.7 23.3 - - + -
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Residues in contact with VAL 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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64B GLY 3.4 10.3 - - - +
65B VAL 4.9 0.2 - - - -
66B LYS* 4.1 38.6 - - + +
85B LEU* 4.0 24.5 - - + -
86B VAL* 1.3 71.2 - - - +
88B ALA* 1.3 61.7 + - - +
89B ALA 4.2 11.9 - - - +
90B ASP* 5.8 2.5 - - - +
205B GLU* 4.2 5.4 - - + -
206B LYS 3.0 17.5 + - - +
207B THR* 3.4 11.7 + - - +
208B ALA 3.0 24.3 + - - -
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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