Contacts of the strand formed by residues 162 - 167 (chain A) in PDB entry 3RAY
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 ARG 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A PRO* 3.7 31.9 - - + +
101A TYR 4.7 7.6 - - - -
105A ILE* 3.5 32.2 - - - +
119A ILE* 4.5 3.6 - - - +
129A ILE* 4.6 10.0 - - - +
158A GLN* 3.2 5.3 - - - +
159A HIS 2.9 34.9 + - - +
160A SER* 3.7 9.3 + - - +
161A GLU* 1.3 105.4 + - - +
163A ILE* 1.3 66.4 - - - +
164A TYR* 3.8 8.1 - - + +
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Residues in contact with ILE 163 (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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100A PRO* 3.3 4.7 - - - +
101A TYR* 2.8 49.1 + - + +
117A TRP* 3.8 32.1 - - + -
118A LEU 3.6 6.7 - - - +
119A ILE* 3.8 16.4 - - + -
129A ILE* 4.9 5.9 - - + +
140A MET* 4.0 0.5 - - - +
156A ALA* 4.5 1.8 - - + -
157A PHE 3.4 8.7 - - - +
158A GLN* 4.3 2.7 - - + -
162A ARG* 1.3 74.0 - - - +
164A TYR* 1.3 67.1 + - - +
165A PHE* 3.9 26.5 - - + -
185A TYR* 3.4 41.7 - - + +
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Residues in contact with TYR 164 (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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30A TRP* 4.7 7.5 - + - -
51A PHE* 4.5 15.9 - + - -
97A ILE* 3.7 15.5 - - + -
98A PHE 3.3 18.2 - - - +
99A GLY 3.7 9.9 - - - -
100A PRO* 3.6 31.6 - - + +
140A MET* 4.2 1.1 - - - -
156A ALA* 3.3 3.8 - - - -
157A PHE* 2.9 53.9 + + + -
159A HIS* 3.5 41.8 + - + -
160A SER* 5.9 1.2 - - - -
162A ARG* 3.8 15.8 - - + +
163A ILE* 1.3 76.5 - - - +
165A PHE* 1.3 66.8 + - - +
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Residues in contact with PHE 165 (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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97A ILE* 3.6 0.9 - - - -
98A PHE* 2.8 40.9 + - + +
101A TYR* 4.3 3.6 - + - -
117A TRP* 3.8 38.6 - + - -
139A TRP* 5.0 3.1 - + - -
140A MET* 3.6 45.1 - - + +
143A VAL* 3.8 27.6 - - + -
154A LEU* 4.1 31.0 - - + -
155A LEU 3.4 5.4 - - - +
156A ALA* 3.8 12.3 - - + -
157A PHE* 4.2 2.0 - - - -
163A ILE* 3.9 9.4 - - + -
164A TYR* 1.3 81.1 - - - +
166A ARG* 1.3 58.9 + - - +
179A VAL* 3.9 11.4 - - + -
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Residues in contact with ARG 166 (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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31A PHE* 3.8 43.5 + - - +
33A GLU* 2.7 45.7 + - + +
95A GLY* 4.7 4.3 - - - +
96A HIS 3.3 8.5 - - - +
97A ILE* 4.3 11.4 - - + +
154A LEU* 3.3 4.4 - - - -
155A LEU* 2.9 54.1 + - + +
157A PHE* 3.7 38.1 - - + +
165A PHE* 1.3 73.6 - - - +
167A ALA* 1.3 65.8 + - - +
168A CYS 3.3 0.7 + - - -
182A SER* 3.7 27.5 + - - -
184A ASP* 4.4 8.3 + - - +
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Residues in contact with ALA 167 (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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33A GLU* 3.6 6.1 - - - +
92A ILE* 4.2 9.0 - - + -
93A PRO 3.7 19.1 - - - +
95A GLY* 2.8 27.3 + - - +
96A HIS 2.9 14.7 + - - +
98A PHE* 4.7 0.4 - - + -
153A ASN 3.2 10.3 - - - +
154A LEU* 3.8 6.1 - - + +
166A ARG* 1.3 70.1 - - - +
168A CYS* 1.3 57.6 + - - +
169A ARG 3.3 18.6 - - - +
171A ILE* 4.0 14.1 - - + -
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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