Contacts of the strand formed by residues 159 - 164 (chain D) in PDB entry 3P3W
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 GLN 159 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLU 2.9 9.0 + - - +
132D LYS* 4.1 23.1 - - + +
133D PHE* 3.1 28.1 + - - +
157D ASN 4.0 1.5 + - - +
158D TRP* 1.3 69.3 - - - +
160D VAL* 1.3 62.6 + - - +
161D THR* 4.1 2.0 - - + -
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Residues in contact with VAL 160 (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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160B VAL 5.8 0.3 - - - +
133D PHE* 3.8 29.6 - - + -
135D TYR* 3.7 26.7 - - + -
149D ILE* 4.1 18.4 - - + -
150D MET* 5.1 10.8 - - + +
153D ALA* 3.7 29.2 - - + -
158D TRP* 3.4 6.4 + - + +
159D GLN* 1.3 74.4 - - - +
161D THR* 1.3 65.5 + - - +
162D ALA* 3.7 11.6 + - + +
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Residues in contact with THR 161 (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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154B VAL* 5.3 10.8 - - + -
133D PHE 3.6 15.6 + - - -
134D VAL* 3.8 16.1 - - - +
135D TYR* 2.9 21.5 + - - +
159D GLN* 5.2 3.3 + - + +
160D VAL* 1.3 74.1 - - - +
162D ALA* 1.3 61.6 + - - +
163D ARG* 3.5 6.6 + - - +
181D MET* 4.2 21.9 - - + -
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Residues in contact with ALA 162 (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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150B MET* 3.5 27.7 - - - +
154B VAL* 5.4 1.2 - - - +
135D TYR* 3.3 25.4 - - + -
137D TYR* 3.6 18.6 - - + -
146D LEU* 4.3 0.4 - - + -
150D MET* 3.9 27.8 - - + -
160D VAL* 3.7 5.7 + - + +
161D THR* 1.3 71.9 - - - +
163D ARG* 1.3 64.2 + - - +
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Residues in contact with ARG 163 (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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150B MET 3.7 18.9 + - - -
151B GLU* 4.0 31.2 + - - +
154B VAL* 3.7 25.9 - - + +
134D VAL* 6.0 1.3 - - + -
135D TYR 2.9 8.5 + - - +
136D LEU* 3.7 25.4 - - + -
137D TYR* 3.1 28.9 + - - +
161D THR* 4.6 6.7 - - - +
162D ALA* 1.3 76.6 - - - +
164D SER* 1.3 69.5 + - - +
165D VAL* 3.2 9.0 + - + +
168D ILE* 4.4 13.7 - - - +
177D ILE* 3.4 46.6 - - + +
180D GLU* 5.3 4.6 + - - -
181D MET* 6.0 5.4 - - + -
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Residues in contact with SER 164 (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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147B GLN* 2.7 37.3 + - - -
150B MET* 5.4 2.7 - - - +
151B GLU* 4.8 14.5 + - - +
137D TYR* 3.7 21.3 + - - -
162D ALA 4.3 0.2 + - - -
163D ARG* 1.3 79.0 + - - +
165D VAL* 1.3 60.3 + - - +
166D GLY 4.3 1.6 + - - -
167D ASN* 3.3 22.4 + - - +
168D ILE* 3.8 17.2 + - - +
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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