Contacts of the strand formed by residues 78 - 82 (chain A) in PDB entry 1EKP
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLU* 5.8 0.4 - - - -
77A GLY* 1.3 77.2 - - - +
79A LYS* 1.3 64.0 + - - +
90A LEU* 3.7 28.5 - - + -
91A PHE 5.1 4.9 - - - +
93A PRO* 3.5 33.2 - - + +
96A ASN* 3.7 34.3 - - - +
97A MET* 4.3 15.3 - - + -
118A LEU* 5.0 2.0 - - + -
121A ILE* 5.1 7.6 - - + -
141A TYR* 3.6 7.2 - - - -
142A VAL* 2.7 51.8 + - + +
144A PRO* 5.1 6.5 - - + -
313A THR* 4.1 7.6 - - - -
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 5.4 2.0 - - - -
78A MET* 1.3 78.2 - - - +
80A ALA* 1.3 60.1 + - - +
81A PHE* 3.8 29.8 - - + -
90A LEU* 3.5 9.4 - - - +
91A PHE* 3.3 27.9 + - + +
139A SER* 3.3 24.5 + - - +
140A LEU 3.2 7.2 - - - +
141A TYR* 4.3 10.3 - - + -
142A VAL* 5.0 0.4 - - - -
170A VAL* 4.3 14.5 - - - +
171A GLY 5.5 3.6 + - - -
172A ALA* 6.4 0.2 - - - +
173A TYR 6.1 0.8 - - - +
313A THR* 3.0 46.6 + - + +
314A ALA* 3.4 17.6 + - - +
316A GLN* 4.4 7.0 - - - +
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LYS* 1.3 73.7 - - - +
81A PHE* 1.3 62.5 + - - +
88A VAL* 4.1 17.9 - - + -
89A ARG 3.1 9.0 - - - +
90A LEU* 3.5 20.9 - - + -
125A ILE* 4.6 3.6 - - + -
132A VAL* 4.2 2.7 - - + +
139A SER* 3.3 5.9 - - - -
140A LEU* 2.9 52.8 + - + +
142A VAL* 4.8 0.4 - - + -
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LYS* 3.8 36.3 - - + -
80A ALA* 1.3 75.6 - - - +
82A LYS* 1.3 60.1 + - - +
83A GLY 3.2 5.7 + - - -
88A VAL* 3.3 1.9 - - - -
89A ARG* 2.8 42.8 + - - +
91A PHE* 4.1 8.7 - - + -
132A VAL* 4.4 1.8 - - - -
137A GLY 5.8 0.9 - - - -
138A THR 4.1 0.2 - - - -
139A SER* 3.7 24.9 - - - +
316A GLN* 4.5 6.1 - - + -
353A GLN* 3.5 66.0 - - + +
354A TYR* 3.7 35.0 - + + -
362A MET* 4.3 3.4 - - + -
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 1.3 69.3 - - - +
83A GLY* 1.3 77.3 + - - +
84A LYS* 3.7 0.7 + - - +
86A GLN* 4.0 30.5 + - - +
87A GLN 3.6 3.4 - - - -
88A VAL* 4.1 11.0 - - + -
129A LYS* 3.4 26.3 + - - +
130A ASP* 4.4 9.5 + - - +
132A VAL* 2.8 41.7 + - + +
133A PRO 3.3 18.6 + - - +
134A ASP* 3.8 30.3 - - + +
138A THR 5.4 0.6 + - - -
354A TYR* 3.8 16.5 - - - -
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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