Contacts of the strand formed by residues 158 - 165 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLU* 4.4 13.5 - - + +
152D VAL* 3.6 26.0 - - + -
153D ARG* 3.7 31.2 - - + -
156D GLY 3.8 8.7 - - - +
157D SER* 1.3 75.6 - - - +
159D GLU* 1.3 61.0 + - - +
160D ARG 3.9 15.7 - - - +
161D CYS* 4.3 12.6 - - + -
178D ALA* 3.9 7.9 - - + -
179D GLU 3.4 13.2 - - - +
180D TYR* 3.9 15.7 - - + -
181D MET* 3.8 13.1 - - - +
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Residues in contact with GLU 159 (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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54D GLN* 4.5 2.3 + - - -
57D ASN* 4.2 19.6 + - - +
59D ARG* 3.3 40.4 + - - +
60D LYS* 4.1 25.6 - - + +
99D THR* 4.3 1.7 - - - +
158D LEU* 1.3 73.7 - - - +
160D ARG* 1.3 68.6 + - + +
179D GLU* 2.6 27.5 + - + +
180D TYR 3.6 21.3 - - - +
181D MET* 3.0 28.7 - - - +
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Residues in contact with ARG 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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54D GLN* 3.0 35.4 - - - +
55D PHE* 2.8 49.4 + - - +
57D ASN* 3.7 19.1 - - + +
58D ARG* 3.4 24.4 - - - +
130D THR* 4.1 9.7 + - - -
133D LEU* 4.1 18.5 - - + +
158D LEU* 3.9 4.5 - - - +
159D GLU* 1.3 85.2 - - + +
161D CYS* 1.3 64.5 + - - +
162D PHE* 4.4 16.0 - - + -
177D PHE 4.6 0.9 - - - -
178D ALA* 3.7 0.5 - - - -
179D GLU* 2.7 63.3 + - + +
213D LEU* 6.3 1.4 - - - +
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Residues in contact with CYS 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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50D HIS* 4.7 0.2 - - - -
54D GLN* 2.6 22.7 + - - +
145D GLN* 3.1 16.3 - - - +
148D PHE* 3.6 28.7 - - - -
149D GLU* 3.8 33.7 - - + -
152D VAL* 4.2 10.8 - - - -
158D LEU* 4.3 16.8 - - + -
160D ARG* 1.3 78.7 - - - +
162D PHE* 1.3 64.8 + - - +
177D PHE 3.4 7.6 - - - +
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Residues in contact with PHE 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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51D THR* 3.8 22.2 - - + +
54D GLN* 3.6 30.3 - - + -
55D PHE* 3.8 31.0 - + + -
133D LEU* 5.7 2.9 - - + -
145D GLN* 3.3 6.7 - - - +
148D PHE* 4.0 4.7 - - - -
160D ARG* 4.4 17.9 - - + -
161D CYS* 1.3 82.7 - - - +
163D LEU* 1.3 70.7 + - - +
164D VAL* 4.1 2.7 - - + -
176D GLY* 3.2 1.7 - - - -
177D PHE* 2.9 65.6 + + + -
213D LEU* 5.2 1.3 - - + -
218D LEU* 3.4 26.9 - - + -
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Residues in contact with LEU 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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51D THR* 2.8 27.3 + - - +
139D LEU* 3.3 33.9 - - + -
143D LEU* 4.0 8.1 - - + +
144D THR 3.4 8.3 - - - +
145D GLN* 3.0 56.1 - - + +
148D PHE* 3.5 22.0 - - + -
162D PHE* 1.3 77.4 - - - +
164D VAL* 1.3 60.4 + - - +
165D TYR* 4.1 18.8 - - + +
172D SER* 4.1 16.8 - - - +
175D TYR 3.7 9.4 - - - +
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Residues in contact with VAL 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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51D THR* 5.0 4.0 - - + -
162D PHE* 4.1 10.1 - - + -
163D LEU* 1.3 78.7 - - - +
165D TYR* 1.3 62.7 + - - +
172D SER* 3.7 0.7 - - - -
173D LYS* 2.8 38.2 + - + +
175D TYR* 3.2 38.7 + - + +
177D PHE* 3.6 35.7 - - + -
218D LEU* 3.7 18.6 - - + +
219D HIS* 4.1 17.5 - - + +
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Residues in contact with TYR 165 (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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47D ARG* 3.5 55.4 - - + +
48D LEU* 4.0 19.8 - - + +
50D HIS* 5.9 2.1 - - + +
51D THR* 3.3 27.5 - - - +
143D LEU 6.0 0.4 - - - -
144D THR* 6.5 0.4 - - - -
145D GLN* 3.3 31.1 + - - +
163D LEU* 4.1 16.9 - - + +
164D VAL* 1.3 76.0 - - - +
166D SER* 1.3 65.3 + - - +
167D GLU 3.7 0.2 + - - -
170D GLY* 3.4 24.2 - - - +
171D GLN 3.4 7.2 - - - +
172D SER* 3.5 22.9 - - - -
173D LYS* 4.0 4.3 - - - -
219D HIS* 3.2 21.7 - - - -
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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