Contacts of the strand formed by residues 75 - 83 (chain A) in PDB entry 1OXC
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 ASP 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PRO 4.1 1.0 + - - -
74A SER* 1.3 71.3 - - - +
76A LEU* 1.3 65.4 + - - +
94A SER* 3.2 5.7 - - - -
95A GLU* 2.9 35.7 + - + +
102A TYR* 2.6 36.9 + - + +
1C ALA* 2.7 26.5 + - - +
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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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3A GLN* 3.5 41.1 - - + +
4A GLY* 4.2 5.4 - - - -
65A VAL 3.2 28.5 - - - +
66A GLN* 4.4 5.8 - - + -
67A VAL* 4.0 19.1 - - + +
74A SER 3.8 13.9 - - - +
75A ASP* 1.3 85.1 + - - +
77A VAL* 1.3 70.9 + - - +
92A VAL* 4.2 9.2 - - + -
93A GLY 3.4 5.8 - - - +
94A SER* 3.6 25.8 - - - -
102A TYR* 4.6 0.2 - - - -
1C ALA 4.6 3.5 + - - -
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Residues in contact with VAL 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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3A GLN* 3.3 10.5 - - - +
76A LEU* 1.3 75.4 - - - +
78A SER* 1.3 64.3 + - - +
92A VAL* 3.3 2.4 - - - +
93A GLY* 2.8 50.1 + - - +
102A TYR* 3.8 16.2 - - + -
83B LEU* 4.0 25.4 - - + +
84B THR* 4.0 13.2 - - + +
87B LEU* 4.2 4.9 - - + -
1C ALA* 3.2 35.2 - - + -
3C GLN* 5.0 4.0 - - - +
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Residues in contact with SER 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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3A GLN* 2.9 27.3 + - - +
4A GLY* 2.8 31.5 + - - -
5A VAL 5.5 0.3 + - - -
6A PHE* 3.7 14.4 - - - -
77A VAL* 1.3 75.8 - - - +
79A ALA* 1.3 67.6 + - - +
91A LEU 3.0 16.4 - - - -
92A VAL* 4.1 2.0 - - - -
83B LEU* 3.8 11.3 - - - +
83D LEU* 4.9 4.7 - - - +
84D THR* 5.0 5.3 + - - -
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Residues in contact with ALA 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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6A PHE* 3.8 7.2 - - - -
78A SER* 1.3 79.7 - - - +
80A GLN* 1.3 61.6 + - - +
81A VAL* 5.2 1.8 - - + -
89A PHE 3.9 0.5 - - - +
90A ALA* 3.7 1.2 - - - -
91A LEU* 2.9 33.8 + - + +
81B VAL* 4.8 7.4 - - + -
83B LEU* 3.7 21.6 - - + +
79C ALA* 4.9 0.2 - - + -
81D VAL* 4.5 9.0 - - + -
82D ILE 3.6 12.8 - - - +
83D LEU* 4.2 13.5 - - + +
84D THR 5.7 0.9 - - - +
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Residues in contact with GLN 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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6A PHE* 4.5 14.8 - - + +
7A THR 4.4 10.8 + - - +
79A ALA* 1.3 74.4 - - - +
81A VAL* 1.3 64.9 + - - +
82A ILE* 3.7 12.8 - - + +
88A ASN* 2.8 29.5 - - - +
89A PHE 3.1 17.9 - - - +
90A ALA* 4.3 2.0 - - + +
111A TRP* 3.6 20.2 - - + -
81D VAL* 3.2 7.6 - - - +
82D ILE* 2.8 60.7 + - + +
85D ASN* 4.4 10.4 - - - +
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Residues in contact with VAL 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 ALA 5.2 1.1 - - - -
80A GLN* 1.3 79.7 - - - +
82A ILE* 1.3 66.4 + - - +
83A LEU* 4.0 24.9 - - + -
87A LEU 3.6 1.2 - - - +
88A ASN* 3.5 2.9 - - - +
89A PHE* 2.9 34.9 + - + +
91A LEU* 4.7 5.8 - - + -
79B ALA* 4.8 7.9 - - + -
81B VAL* 4.2 31.0 - - + -
91B LEU* 4.3 19.5 - - + -
81C VAL* 5.5 5.8 - - + -
79D ALA* 4.8 4.9 - - + -
80D GLN 3.3 8.5 - - - +
81D VAL* 4.4 12.8 - - + -
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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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80A GLN* 3.7 13.2 - - + +
81A VAL* 1.3 76.9 - - - +
83A LEU* 1.3 65.4 + - - +
85A ASN* 3.9 13.3 + - - +
86A GLU* 3.6 24.0 - - - +
87A LEU 3.2 7.0 - - - +
88A ASN* 3.2 31.4 - - - +
79D ALA* 3.6 5.9 - - - +
80D GLN* 2.8 71.3 + - + +
82D ILE* 4.5 4.7 - - + -
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Residues in contact with LEU 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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81A VAL* 4.0 12.3 - - + -
82A ILE* 1.3 79.0 - - - +
84A THR* 1.3 72.6 + - - +
85A ASN 3.0 2.7 + - - -
87A LEU* 2.8 34.1 + - + +
89A PHE* 3.9 27.6 - - + -
77B VAL* 3.9 28.5 - - + +
78B SER* 3.9 31.0 - - - +
79B ALA* 3.8 25.6 - - + +
91B LEU* 4.5 6.5 - - + +
93B GLY 4.8 0.9 - - - +
78D SER 4.8 2.7 - - - +
79D ALA* 4.1 11.0 - - + +
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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