Contacts of the strand formed by residues 78 - 82 (chain B) in PDB entry 1EKF
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 MET 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLY* 1.3 76.1 - - - +
79B LYS* 1.3 64.4 + - - +
90B LEU* 4.3 16.8 - - + -
91B PHE 4.9 4.5 - - - +
93B PRO* 4.0 18.6 - - + -
96B ASN* 3.5 39.0 - - - +
97B MET* 4.0 10.5 - - + -
118B LEU* 4.9 0.9 - - + -
121B ILE* 3.8 43.3 - - + -
141B TYR* 3.7 5.3 - - - -
142B VAL* 2.8 47.6 + - + +
144B PRO* 4.8 4.0 - - + -
313B THR* 4.0 9.2 - - - -
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Residues in contact with LYS 79 (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 PHE* 6.3 0.4 - - - -
78B MET* 1.3 77.1 - - - +
80B ALA* 1.3 59.7 + - - +
81B PHE* 3.7 32.0 - - + -
90B LEU* 3.4 9.6 - - - +
91B PHE* 3.2 27.7 + - + +
137B GLY 5.6 3.0 + - - -
139B SER* 3.2 27.4 + - - +
140B LEU 3.3 7.9 - - - +
141B TYR* 4.3 13.0 - - + -
170B VAL* 5.0 15.8 - - - +
172B ALA* 6.3 1.2 - - - +
173B TYR* 5.8 0.6 - - - +
313B THR* 3.1 43.6 + - + +
314B ALA* 3.7 17.6 + - - +
316B GLN* 5.2 5.3 - - - +
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Residues in contact with ALA 80 (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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79B LYS* 1.3 73.2 - - - +
81B PHE* 1.3 61.6 + - - +
88B VAL* 3.8 21.1 - - + -
89B ARG 3.2 6.1 - - - +
90B LEU* 3.7 17.0 - - + +
125B ILE* 4.0 14.4 - - + -
132B VAL* 4.0 3.1 - - - +
139B SER* 3.5 3.5 - - - -
140B LEU* 2.9 47.3 + - + +
142B VAL* 4.8 0.4 - - + +
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Residues in contact with PHE 81 (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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79B LYS* 3.7 39.0 - - + -
80B ALA* 1.3 75.5 - - - +
82B LYS* 1.3 60.5 + - - +
83B GLY 3.8 0.7 + - - -
87B GLN 3.5 1.7 - - - +
88B VAL* 3.2 4.1 - - - -
89B ARG* 2.8 43.3 + - - +
91B PHE* 3.8 18.2 - + + -
132B VAL* 4.8 0.2 - - - -
139B SER* 3.9 16.8 - - - +
316B GLN* 4.3 6.3 - - - -
353B GLN* 3.3 60.7 - - + +
354B TYR* 3.5 40.6 - + + -
362B MET* 4.3 3.6 - - + -
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Residues in contact with LYS 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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81B PHE* 1.3 72.9 - - - +
83B GLY* 1.3 71.3 + - - +
86B GLN* 2.8 55.4 - - - +
87B GLN 3.2 4.5 - - - +
88B VAL* 3.8 19.1 - - + +
129B LYS* 3.3 21.1 + - - +
130B ASP* 4.3 8.1 + - - +
132B VAL* 3.0 34.8 + - + +
133B PRO 3.5 14.9 + - - +
134B ASP* 3.9 20.1 + - + +
138B THR 5.5 0.6 + - - -
354B TYR* 3.6 18.2 - - - -
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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