Contacts of the strand formed by residues 149 - 154 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASP* 4.5 4.7 - - - +
105A LYS* 2.7 31.1 + - - +
147A THR* 3.1 11.7 + - - +
148A ARG* 1.3 113.4 - - - +
150A CYS* 1.3 60.4 + - - +
151A ILE* 4.2 4.5 - - + -
163A ILE 3.7 1.8 - - - -
164A VAL* 3.8 26.5 - - + -
254A PHE* 4.0 19.3 - + - -
255A ASN* 3.7 31.4 - - - -
258A SER* 5.3 10.1 - - - -
1385A NAD 3.5 32.3 - - - +
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Residues in contact with CYS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 3.3 31.6 - - - -
105A LYS* 4.0 11.4 - - + -
106A ALA* 3.8 16.8 - - - -
149A PHE* 1.3 77.4 - - - +
151A ILE* 1.3 60.9 + - - +
152A ILE* 3.8 18.3 + - - -
161A MET 3.8 0.5 - - - +
162A ALA 3.8 0.2 - - - -
163A ILE* 2.8 56.2 + - + +
168A VAL* 4.3 9.0 - - + -
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 3.5 21.8 - - - +
102A ASP* 3.0 17.5 + - - +
149A PHE* 5.1 2.0 - - + -
150A CYS* 1.3 77.7 - - - +
152A ILE* 1.3 61.8 + - - +
153A THR* 4.1 1.6 + - - -
160A LYS* 4.1 36.5 - - + +
161A MET 3.2 16.4 - - - +
162A ALA* 4.8 11.2 - - + -
267A HIS* 5.0 10.1 - - + +
1385A NAD 3.4 47.3 - - + +
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 4.4 8.1 - - + -
73A THR 3.8 4.9 - - - +
74A VAL* 3.6 38.8 - - + +
77A VAL* 4.0 10.5 - - + -
102A ASP 3.5 30.5 - - - +
103A CYS* 4.2 3.1 - - - +
106A ALA* 3.7 15.9 - - + -
117A VAL* 4.0 20.4 - - + -
150A CYS* 3.8 16.0 + - - -
151A ILE* 1.3 78.0 - - - +
153A THR* 1.3 65.6 + - - +
160A LYS* 4.6 0.7 - - - -
161A MET* 2.9 37.2 + - + +
163A ILE* 4.7 2.0 - - + +
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Residues in contact with THR 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASN* 3.2 27.4 + - - +
72A PRO* 3.1 20.5 + - - +
73A THR* 3.1 14.4 - - + -
74A VAL* 2.9 27.1 + - - -
151A ILE 4.1 1.2 + - - -
152A ILE* 1.3 71.7 - - - +
154A ASP* 1.3 70.0 + - - +
155A GLU* 3.6 6.9 + - + +
158A HIS* 5.6 2.2 - - - -
159A VAL 4.5 3.4 - - - +
160A LYS* 3.2 31.6 - - + +
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.6 20.4 - - + +
118A LYS* 2.9 27.1 + - - +
152A ILE 3.6 1.4 + - - -
153A THR* 1.3 71.6 - - - +
155A GLU* 1.3 58.5 + - - +
156A VAL* 2.9 24.8 + - - +
157A ARG* 3.2 40.2 + - - +
158A HIS* 3.0 19.2 + - - -
159A VAL 3.1 22.0 + - - +
161A MET* 3.8 10.5 - - + -
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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