Contacts of the strand formed by residues 67 - 75 (chain A) in PDB entry 1J3H
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 ASN 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A VAL 3.6 0.3 - - - +
61A LYS* 3.0 7.1 - - - -
62A HIS* 2.8 29.0 + - + +
65A SER* 3.1 31.4 + - - +
66A GLY* 1.3 80.4 - - - +
68A HIS* 1.3 61.9 + - - +
69A TYR* 3.5 32.8 + - + -
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Residues in contact with HIS 68 (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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46A ILE* 4.4 10.7 - - + +
59A LEU* 4.1 24.5 - - + +
60A VAL 3.4 12.6 - - - +
61A LYS* 3.7 16.3 - - + +
66A GLY 4.7 4.4 + - - -
67A ASN* 1.3 81.4 + - - +
69A TYR* 1.3 72.0 + - - +
122A TYR* 3.8 24.7 + - + +
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Residues in contact with TYR 69 (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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43A PHE* 4.1 14.6 - + + -
59A LEU* 3.7 6.4 - - - +
60A VAL* 3.0 37.0 + - + +
62A HIS* 4.0 13.6 + + + -
65A SER* 4.6 0.9 + - - -
67A ASN* 3.5 38.8 + - + -
68A HIS* 1.3 81.3 - - - +
70A ALA* 1.3 60.7 + - - +
71A MET* 3.7 1.9 + - + +
107A GLU* 3.4 36.0 + - + -
108A PHE* 3.5 34.3 - + - -
119A VAL* 4.4 14.4 - - + -
120A MET 3.2 17.5 - - - +
121A GLU* 4.2 5.4 - - + -
122A TYR* 4.0 7.0 - - - -
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Residues in contact with ALA 70 (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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49A LEU* 4.3 12.3 - - + -
57A VAL* 4.6 8.2 - - + +
58A MET 4.0 4.5 - - - -
69A TYR* 1.3 69.9 - - - +
71A MET* 1.3 63.2 + - - +
72A LYS* 3.4 3.6 + - - +
118A MET 3.4 1.2 - - - +
119A VAL* 4.5 0.2 - - - -
120A MET* 2.9 44.4 + - + +
121A GLU 4.7 0.7 - - - +
122A TYR* 4.1 24.8 - - + +
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Residues in contact with MET 71 (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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40A LEU* 3.7 25.4 - - + -
43A PHE* 4.0 25.4 - - + -
57A VAL* 3.4 3.7 - - - -
58A MET* 2.9 51.8 + - - +
60A VAL* 4.6 12.8 - - + -
69A TYR* 3.7 2.4 - - + +
70A ALA* 1.3 69.7 - - - +
72A LYS* 1.3 61.4 + - - +
73A ILE* 3.5 20.3 + - + +
110A PHE* 4.0 18.6 - - + -
117A TYR* 3.5 29.8 - - + -
118A MET 3.6 8.1 - - - +
119A VAL* 4.1 10.3 - - + +
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Residues in contact with LYS 72 (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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56A ARG 4.0 3.8 - - - -
57A VAL* 4.4 15.5 - - + +
70A ALA 3.4 3.0 + - - +
71A MET* 1.3 70.3 - - - +
73A ILE* 1.3 62.7 + - - +
74A LEU* 3.2 21.9 - - + +
117A TYR* 3.7 0.7 - - - -
118A MET* 2.9 38.3 + - + +
120A MET* 5.2 5.6 - - + -
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Residues in contact with ILE 73 (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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55A GLY* 3.3 17.2 - - - +
56A ARG* 3.0 33.2 + - + +
58A MET* 3.6 25.4 - - + -
71A MET* 3.6 32.1 - - + +
72A LYS* 1.3 72.2 - - - +
74A LEU* 1.3 62.1 + - - +
75A ASP 4.1 0.7 - - - +
115A ASN* 3.4 34.8 - - + +
116A LEU 3.7 4.3 - - - +
117A TYR* 3.9 13.7 - - + -
335A ILE* 6.2 1.8 - - + -
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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
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54A PHE* 3.6 36.8 - - + -
72A LYS* 3.2 23.3 - - + +
73A ILE* 1.3 74.4 - - - +
75A ASP* 1.3 67.5 + - - +
76A LYS 3.3 0.2 + - - -
79A VAL* 4.2 6.6 - - + +
88A THR* 3.6 31.4 - - + +
115A ASN* 3.8 2.9 - - - -
116A LEU* 3.0 53.9 + - + +
118A MET* 4.2 24.9 - - + -
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Residues in contact with ASP 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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54A PHE 3.4 19.9 + - - +
55A GLY* 4.6 2.1 - - - -
73A ILE* 4.1 1.4 - - - +
74A LEU* 1.3 67.2 - - - +
76A LYS* 1.3 61.4 + - - +
77A GLN* 3.8 10.0 + - - +
78A LYS* 3.3 28.7 + - + +
79A VAL* 2.8 34.9 + - - +
114A SER* 4.0 12.0 - - - +
115A ASN* 3.5 19.8 + - - +
336A ARG 5.6 0.3 - - - +
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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