Contacts of the strand formed by residues 62 - 69 (chain D) 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 LYS 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D VAL* 4.1 24.7 - - + -
6D PHE 3.7 7.6 - - - +
7D THR* 4.9 4.0 - - - +
31D LEU 3.7 0.6 - - - +
32D VAL* 3.4 6.2 - - - +
33D ASN* 2.9 29.6 + - - +
34D ASN* 3.0 38.3 + - - +
57D SER 4.1 0.2 + - - -
60D SER* 3.0 18.5 + - - +
61D GLY* 1.3 76.8 - - - +
63D VAL* 1.3 64.7 + - - +
64D GLN* 4.2 19.5 - - + +
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Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GLY 3.8 1.0 - - - +
5D VAL* 3.6 1.9 - - - +
6D PHE* 2.8 41.6 + - + +
8D LEU* 3.9 24.0 - - + -
14D PHE* 3.7 36.8 - - + -
30D VAL* 4.2 9.9 - - + -
31D LEU 3.3 7.6 - - - +
32D VAL* 4.7 4.3 - - + -
57D SER* 4.6 3.6 - - - -
61D GLY 4.0 5.4 - - - +
62D LYS* 1.3 80.5 - - - +
64D GLN* 1.3 65.7 + - - +
65D VAL* 5.1 0.2 - - + -
109D ILE* 3.8 27.6 - - + -
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Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D THR* 5.8 0.3 - - - +
3D GLN 5.0 2.8 - - - +
4D GLY 3.2 9.9 - - - +
5D VAL* 3.7 23.7 - - + +
30D VAL* 3.6 3.1 - - - +
31D LEU* 2.8 61.8 + - + +
34D ASN* 4.8 3.4 + - - -
62D LYS* 4.2 22.2 - - + +
63D VAL* 1.3 76.5 - - - +
65D VAL* 1.3 72.8 + - - +
66D GLN* 4.4 19.8 + - + +
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN 4.9 0.2 - - - +
4D GLY* 2.8 15.7 + - - +
6D PHE* 4.6 1.3 - - + -
28D VAL* 4.3 8.5 - - + -
29D ASN 3.6 4.3 - - - +
30D VAL* 5.0 9.2 - - + -
64D GLN* 1.3 81.2 - - - +
66D GLN* 1.3 72.3 + - - +
67D VAL* 4.3 7.9 - - + -
76D LEU* 3.3 20.0 - - - +
92D VAL* 4.2 22.0 - - + -
107D VAL* 3.9 36.8 - - + -
109D ILE* 3.9 27.8 - - + -
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Residues in contact with GLN 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D THR 3.7 0.8 - - - +
28D VAL* 3.5 4.9 - - - +
29D ASN* 2.8 63.5 + - + +
31D LEU* 3.1 25.2 - - + +
64D GLN* 4.4 16.2 + - + +
65D VAL* 1.3 76.6 - - - +
67D VAL* 1.3 64.8 + - - +
76D LEU* 4.5 4.3 - - + -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLN* 3.6 11.4 - - - +
27D THR 3.3 9.2 - - - +
28D VAL* 4.3 9.0 - - + -
65D VAL* 4.3 13.9 - - + -
66D GLN* 1.3 81.4 - - - +
68D SER* 1.3 67.7 + - - +
73D PRO* 3.5 4.0 - - - +
74D SER* 2.8 32.6 + - - +
76D LEU* 3.9 27.0 - - + +
92D VAL* 5.1 1.6 - - + -
94D SER* 3.6 15.0 - - - +
105D ALA* 3.6 30.5 - - + +
107D VAL* 4.8 4.0 - - + -
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Residues in contact with SER 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLN* 3.9 0.3 - - - -
27D THR* 2.8 52.4 + - - +
67D VAL* 1.3 75.9 - - - +
69D VAL* 1.3 66.2 + - - +
70D ASN 4.1 0.7 - - - -
71D GLY* 4.3 10.1 + - - -
72D ARG 3.2 24.9 - - - -
73D PRO* 4.0 5.4 - - - -
74D SER* 4.1 1.6 - - - +
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Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLY* 4.3 8.5 - - - -
25D THR 3.5 18.8 - - - +
26D GLN* 3.6 30.5 - - - +
68D SER* 1.3 78.0 - - - +
70D ASN* 1.3 85.0 + - - +
72D ARG* 2.9 26.3 + - + +
74D SER* 3.9 4.5 - - - +
96D ASP* 3.6 25.6 - - + -
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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