Contacts of the strand formed by residues 74 - 83 (chain A) in PDB entry 1J71
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 GLN 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A SER 4.2 5.0 + - - +
73A ALA* 1.3 74.5 - - - +
75A ASN* 1.3 63.5 + - - +
76A LEU* 3.4 15.8 + - + +
95A TYR* 3.1 9.0 - - - -
96A LYS* 2.9 67.7 + - + +
108A ASN* 4.4 12.3 + - - -
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Residues in contact with ASN 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 ALA 4.1 1.0 + - - -
74A GLN* 1.3 73.4 - - - +
76A LEU* 1.3 63.4 + - - +
77A ASN* 2.7 54.1 + - - +
93A SER* 4.7 8.3 + - - -
94A PHE 4.0 2.8 - - - +
95A TYR* 3.2 40.8 + - + -
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Residues in contact with LEU 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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74A GLN* 4.0 22.4 - - + +
75A ASN* 1.3 72.6 - - - +
77A ASN* 1.3 71.1 + - - +
78A GLN* 3.2 27.0 + - - +
94A PHE* 3.0 27.5 + - + +
95A TYR 4.1 2.7 - - - +
96A LYS* 3.7 34.3 - - + -
110A GLN* 3.6 42.0 - - + +
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Residues in contact with ASN 77 (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 ASN* 2.7 38.9 + - - +
76A LEU* 1.3 79.0 - - - +
78A GLN* 1.3 59.3 + - - +
79A ASP* 4.3 1.8 + - - +
93A SER* 5.7 2.2 - - - -
94A PHE 4.1 1.2 + - - -
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Residues in contact with GLN 78 (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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76A LEU* 3.2 35.5 + - - +
77A ASN* 1.3 78.5 - - - +
79A ASP* 1.3 63.6 + - - +
93A SER* 3.3 5.1 - - - -
94A PHE* 2.8 46.3 + - + +
110A GLN* 4.5 12.6 + - - +
136A ASN* 5.3 8.8 - - - +
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Residues in contact with ASP 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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77A ASN 4.4 1.5 + - - -
78A GLN* 1.3 77.4 - - - +
80A PHE* 1.3 60.6 + - - +
81A SER* 6.3 0.7 - - - -
92A GLY 3.6 9.9 - - - +
93A SER* 4.4 4.9 - - - +
94A PHE* 3.9 9.9 - - - -
136A ASN* 4.9 4.0 + - - +
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Residues in contact with PHE 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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37A ASP* 3.8 30.5 - - + -
39A TRP* 4.1 18.4 - + + -
79A ASP* 1.3 76.3 - - - +
81A SER* 1.3 64.5 + - - +
82A ILE* 3.5 34.5 - - + -
90A SER 4.2 3.8 - - - -
91A GLN* 3.3 4.2 - - - +
92A GLY 2.8 41.1 + - - +
93A SER* 4.3 1.1 - - - +
94A PHE* 3.4 30.1 - + + -
112A ALA* 3.4 29.6 - - + -
114A VAL* 4.0 22.4 - - + -
133A ALA* 3.9 14.1 - - + -
136A ASN* 5.2 1.6 - - - +
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Residues in contact with SER 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 ASP* 6.3 0.2 - - - -
80A PHE* 1.3 78.2 - - - +
82A ILE* 1.3 63.0 + - - +
90A SER 3.4 6.1 - - - -
91A GLN* 3.7 20.8 + - - +
133A ALA* 3.3 18.1 - - - +
134A GLY* 4.5 5.0 + - - -
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Residues in contact with ILE 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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35A SER* 4.8 3.6 - - - -
37A ASP* 4.0 24.2 - - + +
39A TRP* 4.6 0.7 - - - +
80A PHE* 3.5 28.9 - - + -
81A SER* 1.3 77.5 + - - +
83A GLU* 1.3 69.9 + - - +
84A TYR* 3.5 42.0 - - + +
89A SER* 3.1 7.1 - - - -
90A SER* 3.0 46.0 + - - +
91A GLN* 4.2 0.7 + - - -
133A ALA* 3.9 9.9 - - + -
337B ILE* 4.0 18.6 - - + -
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Residues in contact with GLU 83 (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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82A ILE* 1.3 77.3 - - - +
84A TYR* 1.3 70.9 + - - +
87A LEU* 3.6 31.9 - - - +
88A THR 3.4 13.2 - - - +
89A SER* 4.1 9.2 - - - -
337B ILE* 3.4 7.4 - - - +
338B THR* 2.9 54.6 + - - +
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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