Contacts of the strand formed by residues 156 - 164 (chain B) in PDB entry 3RAW
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 TYR 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B ASP 3.8 0.2 - - - +
151B TRP* 3.3 6.2 - - - -
152B LEU* 2.9 37.8 + - + +
153B GLN* 4.4 2.5 - - + -
155B ARG* 1.3 112.2 + - + +
157B GLU* 1.3 60.4 + - - +
158B ILE 3.8 1.4 + - - -
173B CYS* 4.2 5.4 - - + -
174B LEU 3.4 2.5 - - - -
175B ASP* 3.8 29.7 + - + -
183B VAL* 4.0 26.2 - - + -
185B LEU* 4.1 20.2 - - + -
224B ASP* 3.0 30.0 + - - +
226B PHE* 3.3 39.0 - + - -
235B ALA* 4.0 9.8 - - + +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B GLY* 4.0 20.1 - - - +
150B ASP 3.7 2.7 - - - -
151B TRP* 3.6 26.8 + - + +
155B ARG 3.6 1.0 + - - -
156B TYR* 1.3 72.7 - - - +
158B ILE* 1.3 68.2 + - - +
159B VAL* 3.4 14.2 + - - +
173B CYS* 3.2 3.6 - - - -
174B LEU* 3.0 40.3 + - + +
176B HIS* 3.2 34.3 + - + +
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Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B CYS* 3.8 34.8 - - + -
147B ARG* 3.9 20.6 - - - +
148B ILE* 4.0 8.0 - - + +
149B GLY* 2.8 28.6 + - - -
150B ASP* 3.0 17.5 + - + +
152B LEU* 3.7 26.9 - - + -
156B TYR 3.8 0.8 + - - -
157B GLU* 1.3 71.1 - - - +
159B VAL* 1.3 62.8 + - - +
160B GLY 4.0 9.6 - - - +
161B ASN* 5.7 0.9 - - - +
171B VAL* 4.0 29.2 - - + -
172B GLU 3.5 6.1 - - - +
173B CYS* 3.9 11.7 - - - -
187B ILE* 5.1 0.4 - - + -
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ILE* 4.2 21.1 - - + +
157B GLU* 3.4 20.6 + - - +
158B ILE* 1.3 78.6 - - - +
160B GLY* 1.3 59.5 + - - +
172B GLU* 2.9 46.5 + - + +
173B CYS 4.2 0.4 - - - +
174B LEU* 3.6 32.5 - - + -
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Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ILE* 4.3 10.1 - - - +
158B ILE* 3.8 6.5 - - - +
159B VAL* 1.3 79.8 - - - +
161B ASN* 1.3 61.9 + - - -
162B LEU* 5.3 0.4 - - - -
171B VAL* 3.3 11.3 - - - +
172B GLU* 2.8 36.0 + - - -
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Residues in contact with ASN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B CYS 5.5 1.9 - - - +
147B ARG* 6.2 0.5 - - - -
148B ILE* 5.3 5.0 - - - +
158B ILE* 5.7 1.0 - - - +
160B GLY* 1.3 72.3 - - - -
162B LEU* 1.3 68.5 + - - +
163B GLY 3.7 11.6 + - - +
164B GLU* 4.5 6.5 - - - +
169B LYS* 3.7 27.4 + - - +
170B VAL 3.7 14.8 + - - -
171B VAL* 4.0 13.4 - - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B 3RA 3.9 26.9 - - + +
160B GLY* 5.3 0.7 - - - -
161B ASN* 1.3 79.5 - - - +
163B GLY* 1.3 58.7 + - - +
170B VAL* 2.9 21.4 + - + +
171B VAL 3.9 2.0 - - - -
172B GLU* 3.7 34.5 - - + +
184B ALA* 3.9 17.7 - - + -
238B LEU* 3.4 31.6 - - + -
239B LEU 5.7 1.1 - - - +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B 3RA 4.0 17.5 - - - -
161B ASN* 3.7 5.3 + - - +
162B LEU* 1.3 80.5 - - - +
164B GLU* 1.3 64.9 + - - +
169B LYS* 3.6 1.9 - - - +
170B VAL* 2.8 30.6 + - - +
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Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B 3RA 3.6 21.2 - - - -
143B HIS* 5.5 4.3 - - + -
161B ASN* 4.5 5.6 - - - +
163B GLY* 1.3 80.2 - - - +
165B GLY* 1.3 61.2 + - - +
167B PHE* 4.7 3.4 - - - -
168B GLY 3.6 12.3 - - - +
169B LYS* 4.0 21.5 - - + +
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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