Contacts of the strand formed by residues 149 - 153 (chain D) in PDB entry 3OX4
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 PHE 149 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ASP* 4.6 3.5 - - - +
105D LYS* 2.8 32.7 + - - +
144D SER* 5.7 0.3 - - - -
147D THR* 3.2 17.5 + - - +
148D ARG* 1.3 100.6 - - + +
150D CYS* 1.3 61.1 + - - +
151D ILE* 4.3 7.4 - - + -
163D ILE 3.3 2.9 - - - +
164D VAL* 3.8 30.1 - - + -
168D VAL* 4.3 0.4 - - - -
254D PHE* 3.8 25.4 - + - -
255D ASN* 3.6 37.7 - - - -
258D SER* 4.9 13.5 - - - -
259D LEU* 5.9 0.9 - - + -
1385D NAD 3.9 24.5 - - - +
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Residues in contact with CYS 150 (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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102D ASP* 3.3 29.2 - - - -
105D LYS* 4.0 12.6 - - + -
106D ALA* 3.8 17.7 - - - -
149D PHE* 1.3 75.7 - - - +
151D ILE* 1.3 61.4 + - - +
152D ILE* 3.7 20.5 + - - -
161D MET 3.3 4.2 - - - +
163D ILE* 2.9 55.4 + - + +
168D VAL* 4.4 6.3 - - + -
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Residues in contact with ILE 151 (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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72D PRO* 3.2 25.6 - - - +
102D ASP* 2.6 22.0 + - - +
149D PHE* 4.8 3.6 - - + -
150D CYS* 1.3 80.6 - - - +
152D ILE* 1.3 61.7 + - - +
153D THR* 4.3 0.3 + - - -
160D LYS* 3.3 52.2 + - + +
161D MET 3.5 1.8 - - - +
162D ALA* 3.8 27.1 - - + -
163D ILE 4.7 0.2 - - - +
267D HIS* 5.0 9.0 - - + +
1385D NAD 3.8 41.7 - - + +
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Residues in contact with ILE 152 (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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72D PRO* 3.6 19.3 - - + +
73D THR 3.7 4.3 - - - +
74D VAL* 3.7 37.0 - - + +
77D VAL* 4.0 9.9 - - + -
102D ASP 3.8 20.2 - - - +
103D CYS* 4.2 0.2 - - - -
106D ALA* 3.9 16.2 - - + -
117D VAL* 4.0 20.2 - - + -
150D CYS* 3.7 15.9 + - - +
151D ILE* 1.3 84.6 - - - +
153D THR* 1.3 64.2 + - - +
160D LYS* 4.5 1.1 - - - -
161D MET* 2.8 44.6 + - + +
163D ILE* 5.2 1.1 - - + -
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Residues in contact with THR 153 (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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71D ASN* 3.8 25.1 - - + +
72D PRO 2.8 20.5 + - - -
73D THR* 3.6 10.5 - - + -
74D VAL* 3.2 27.8 + - - +
151D ILE 4.3 0.7 + - - -
152D ILE* 1.3 71.4 - - - +
154D ASP* 1.3 77.8 + - - +
158D HIS* 5.3 2.0 - - - -
159D VAL 4.0 15.7 - - - +
160D LYS* 4.2 15.1 + - + +
271D GLY* 5.2 12.3 - - - +
274D ASN* 5.8 3.6 - - - +
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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