Contacts of the strand formed by residues 70 - 75 (chain J) in PDB entry 2A3W
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 GLU 70 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65J LYS* 3.9 6.0 - - - +
66J GLU* 3.4 28.5 + - + +
67J ARG* 2.8 66.8 + - + +
68J VAL 5.0 1.0 - - - +
69J GLY* 1.3 78.1 - - - +
71J TYR* 1.3 66.7 + - - +
81J THR* 3.8 18.4 - - + +
82J SER 3.7 1.1 - - - -
83J LYS* 3.6 43.8 + - + +
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Residues in contact with TYR 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J LEU* 4.4 8.1 - - + -
63J VAL* 5.3 1.8 - - + -
64J TYR 4.0 2.5 - - - -
65J LYS* 3.4 36.3 + - + +
70J GLU* 1.3 77.7 - - - +
72J SER* 1.3 62.1 - - - +
81J THR* 3.3 2.6 - - - -
82J SER 2.9 41.4 + - - +
84J VAL* 3.7 15.7 - - + -
86J GLU* 2.7 31.6 + - - -
92J VAL* 3.7 20.1 - - - +
94J ILE* 3.5 26.9 - - + -
107J PHE* 3.8 33.3 - + + -
109J ILE* 3.7 27.4 - - + -
114J LEU* 4.4 2.7 - - + -
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Residues in contact with SER 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J LEU 4.3 0.2 - - - -
63J VAL* 3.4 4.7 - - - +
64J TYR* 2.9 38.7 + - - -
66J GLU* 2.8 32.6 + - - +
70J GLU 4.3 0.2 + - - -
71J TYR* 1.3 72.6 - - - +
73J LEU* 1.3 61.3 + - - +
74J TYR* 4.2 15.5 - - - -
79J LYS* 4.2 2.1 - - - -
80J VAL 3.2 7.2 - - - -
81J THR* 2.6 23.6 + - - +
107J PHE* 3.6 6.4 - - - -
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Residues in contact with LEU 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J PHE* 4.2 6.3 - - + -
61J LEU* 3.7 26.7 - - + -
62J LEU 3.3 12.1 - - - +
63J VAL* 4.1 11.4 - - + -
72J SER* 1.3 74.3 - - - +
74J TYR* 1.3 70.0 + - - +
75J ILE* 3.9 20.2 - - + -
78J HIS 3.9 0.2 - - - +
79J LYS* 3.4 1.6 - - - -
80J VAL* 2.9 36.8 + - + +
96J VAL* 3.9 15.0 - - + -
98J TRP* 4.2 9.4 - - + -
105J ALA* 3.8 26.5 - - + -
107J PHE* 3.8 19.5 - - + -
119J LEU* 3.9 3.4 - - + +
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Residues in contact with TYR 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A CPJ 3.2 41.4 - - + +
59J ASN* 3.7 27.1 - - + +
61J LEU* 3.2 8.3 - - - -
62J LEU* 2.8 62.4 + - + +
64J TYR* 4.0 17.7 - + + -
66J GLU* 4.0 5.2 + - - -
72J SER* 4.2 9.4 - - - -
73J LEU* 1.3 77.2 - - - +
75J ILE* 1.3 64.9 + - - +
77J ARG 3.8 18.6 - - - -
78J HIS 3.0 4.7 - - - +
79J LYS* 3.6 41.4 - - + -
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Residues in contact with ILE 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J PHE* 3.6 37.2 - - + -
60J GLU 3.4 4.0 - - - +
61J LEU* 4.6 2.7 - - + -
73J LEU* 3.9 19.1 - - + -
74J TYR* 1.3 80.4 - - - +
76J GLY* 1.3 68.5 + - - +
77J ARG 3.2 0.9 - - - -
78J HIS 2.8 16.1 + - - +
98J TRP* 3.9 33.9 - - + -
119J LEU* 3.7 14.8 - - + +
120J ARG* 3.0 18.9 - - + +
123J TYR* 3.7 25.4 - - + -
125J VAL* 4.0 12.1 - - + -
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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