Contacts of the strand formed by residues 158 - 165 (chain B) in PDB entry 3H2U
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 LEU 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG* 5.7 0.5 + - - -
149B GLU* 4.2 18.8 - - + +
152B VAL* 3.6 27.1 - - + -
153B ARG* 3.6 35.0 - - + -
156B GLY 3.4 0.4 + - - -
157B SER* 1.3 76.2 + - - +
159B GLU* 1.3 60.9 + - - +
160B ARG 4.1 10.5 - - - +
161B CYS* 4.2 8.5 - - + -
178B ALA* 3.9 11.7 - - + -
179B GLU 3.3 15.7 - - - +
180B TYR* 3.8 17.9 - - + +
181B MET* 4.0 11.0 - - - +
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Residues in contact with GLU 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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54B GLN* 4.6 3.0 + - - -
57B ASN* 4.4 17.0 + - - +
59B ARG* 3.1 37.4 + - - +
60B LYS* 3.9 24.2 - - + +
99B THR* 4.2 3.5 - - - +
157B SER 3.8 0.2 + - - -
158B LEU* 1.3 75.4 - - - +
160B ARG* 1.3 70.0 + - + +
179B GLU* 2.7 29.7 + - + +
180B TYR 3.8 21.1 - - - +
181B MET* 2.8 29.5 - - - +
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Residues in contact with ARG 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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54B GLN* 3.1 35.2 - - - +
55B PHE* 3.0 39.3 + - - +
57B ASN* 3.7 20.4 - - + +
58B ARG* 3.3 25.5 - - - +
130B THR* 3.9 15.0 + - - -
133B LEU* 3.9 19.2 - - + +
158B LEU* 4.1 2.0 - - - +
159B GLU* 1.3 88.1 - - + +
161B CYS* 1.3 62.1 + - - +
162B PHE* 4.6 10.8 - - + -
177B PHE 3.9 1.0 - - - +
178B ALA* 3.6 1.7 - - - -
179B GLU* 2.8 63.7 + - + +
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Residues in contact with CYS 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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50B HIS* 4.5 0.5 - - - -
54B GLN* 2.8 26.9 + - - +
145B GLN* 3.3 18.4 - - - +
148B PHE* 3.7 26.9 - - - -
149B GLU* 3.9 26.5 - - + -
152B VAL* 4.3 8.7 - - - -
158B LEU* 4.2 18.4 - - + -
160B ARG* 1.3 76.9 - - - +
162B PHE* 1.3 66.0 + - - +
177B PHE 3.2 5.8 - - - +
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Residues in contact with PHE 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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50B HIS* 5.4 0.2 - - - +
51B THR* 3.9 22.7 - - + +
54B GLN* 3.7 27.6 - - + -
55B PHE* 3.8 33.7 - + + -
133B LEU* 5.8 2.9 - - + -
145B GLN* 3.3 7.4 - - - +
148B PHE* 4.1 2.9 - - - -
160B ARG* 4.6 14.1 - - + -
161B CYS* 1.3 82.4 - - - +
163B LEU* 1.3 73.8 + - - +
164B VAL* 4.0 3.4 - - + -
176B GLY* 3.1 1.8 - - - -
177B PHE* 2.9 67.4 + + + -
213B LEU* 5.5 1.1 - - + -
218B LEU* 3.5 25.6 - - + -
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Residues in contact with LEU 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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51B THR* 2.9 22.9 + - - +
139B LEU* 3.5 32.5 - - + -
143B LEU* 3.7 11.0 - - + +
144B THR* 3.3 10.8 - - - +
145B GLN* 2.8 54.4 - - + +
148B PHE* 3.6 19.0 - - + -
162B PHE* 1.3 82.3 - - - +
164B VAL* 1.3 59.7 + - - +
165B TYR* 4.0 21.0 + - + +
172B SER* 4.0 17.3 - - - +
175B TYR 3.6 8.1 - - - +
176B GLY* 3.8 0.2 - - - -
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Residues in contact with VAL 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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51B THR* 5.2 3.1 - - + -
162B PHE* 4.0 11.0 - - + -
163B LEU* 1.3 78.2 - - - +
165B TYR* 1.3 56.9 + - - +
172B SER* 3.8 0.4 - - - -
173B LYS* 2.7 39.2 + - + +
175B TYR* 2.9 41.9 + - + +
177B PHE* 4.0 23.3 - - + -
218B LEU* 3.8 25.6 - - + +
219B HIS* 3.9 26.7 - - + +
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Residues in contact with TYR 165 (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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47B ARG* 3.7 53.0 + - + +
48B LEU* 3.8 24.8 - - + +
50B HIS* 6.0 0.9 - - + -
51B THR* 3.4 27.0 - - - +
144B THR* 6.4 0.2 - - - -
145B GLN* 3.3 33.3 + - - +
163B LEU* 4.0 20.1 - - + +
164B VAL* 1.3 76.2 - - - +
166B SER* 1.3 64.1 + - - +
167B GLU* 3.6 0.5 + - - +
170B GLY 3.5 18.2 - - - +
171B GLN 3.3 7.0 - - - +
172B SER* 3.5 27.1 - - - -
173B LYS* 4.0 3.6 - - - -
219B HIS* 3.2 20.8 - - - -
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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