Contacts of the strand formed by residues 72 - 76 (chain A) in PDB entry 1EV2
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 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 4.5 1.4 - - + +
35A HIS 5.3 1.3 - - - +
36A PRO 5.6 2.2 - - - +
38A GLY* 5.5 1.3 - - - -
66A LYS* 3.3 4.0 - - - +
67A GLY* 2.8 29.1 + - - -
70A ALA* 3.1 15.4 - - + +
71A ASN* 1.3 78.5 - - - +
73A TYR* 1.3 65.4 + - - +
84A ALA* 3.6 28.7 - - + +
85A SER 3.3 14.1 - - - +
86A LYS* 4.5 2.0 - - - +
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 4.4 17.9 - - - -
65A ILE 3.6 3.4 - - - +
66A LYS* 3.7 50.4 + - + +
71A ASN 5.3 0.7 - - - -
72A ARG* 1.3 74.7 - - - +
74A LEU* 1.3 65.8 + - - +
75A ALA* 3.5 0.5 + - - +
84A ALA* 3.1 3.0 - - - -
85A SER* 2.7 48.1 + - - +
86A LYS 3.9 16.4 - - - -
87A SER* 4.9 0.2 - - - -
88A VAL* 3.3 33.2 - - + -
92A CYS* 4.1 19.1 - - + -
317E VAL* 3.8 26.3 + - + +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.5 10.5 - - + -
34A ILE* 3.9 19.6 - - + +
40A VAL* 3.9 37.2 - - + -
65A ILE* 2.8 40.3 + - + +
73A TYR* 1.3 74.0 - - - +
75A ALA* 1.3 66.9 + - - +
82A LEU* 4.4 10.5 - - + -
83A LEU 3.6 4.0 - - - +
84A ALA* 4.3 0.2 - - - +
92A CYS* 3.3 20.8 - - - +
94A PHE* 3.8 25.8 - - + -
116A VAL* 4.0 27.6 - - + -
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Residues in contact with ALA 75 (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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73A TYR 4.1 2.5 - - - +
74A LEU* 1.3 77.9 - - - +
76A MET* 1.3 61.4 + - - +
81A ARG 3.8 0.3 - - - +
82A LEU* 3.4 10.1 - - - +
83A LEU* 2.7 52.1 + - + +
85A SER* 4.9 2.7 - - - -
89A THR* 5.2 0.7 - - - +
91A GLU* 3.0 21.1 - - + +
92A CYS* 3.5 16.4 - - - -
94A PHE* 4.2 3.4 - - - -
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Residues in contact with MET 76 (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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75A ALA* 1.3 74.5 - - - +
77A LYS* 1.3 67.0 + - - +
80A GLY* 4.2 9.0 - - - -
81A ARG 3.4 6.3 - - - +
82A LEU* 3.7 23.8 - - + -
91A GLU* 3.0 23.4 + - - +
94A PHE* 4.1 17.6 - - + -
108A SER* 4.1 17.3 - - - +
111A TYR* 3.2 23.5 - - + -
114A TRP* 3.5 25.6 - - + +
115A TYR 3.4 34.8 - - - +
116A VAL* 4.1 2.9 - - - +
125A LYS 5.8 0.2 - - - +
127A GLY* 3.9 15.5 - - - +
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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