Contacts of the strand formed by residues 161 - 167 (chain D) in PDB entry 4S10
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 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D GLN* 1.3 79.5 - - - +
162D LEU* 1.3 60.7 + - - +
163D PHE* 3.1 38.8 - - + -
175D GLU* 3.6 24.1 + - - +
178D VAL* 3.6 7.4 - - - -
190D ILE 4.4 0.4 - - - -
191D LEU* 3.3 8.0 - - - +
192D ASP* 2.8 58.1 + - + +
220D ILE* 4.2 5.1 - - - +
224D GLU* 2.8 36.2 + - - -
225D ARG* 3.6 3.3 - - - +
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Residues in contact with LEU 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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161D ARG* 1.3 75.1 - - - +
163D PHE* 1.3 60.4 + - - +
175D GLU* 3.0 11.2 - - - +
176D VAL* 2.8 54.7 + - + +
177D PRO 3.1 20.9 - - - +
178D VAL* 3.7 8.9 - - + +
179D SER 3.8 6.7 - - - +
182D SER* 3.7 11.4 - - - -
183D PHE* 3.4 40.8 - - + -
189D PHE* 3.8 11.2 - - + -
190D ILE 3.5 22.4 - - - +
191D LEU* 4.0 12.1 - - + +
247D LEU* 5.3 0.9 - - + -
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Residues in contact with PHE 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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161D ARG* 3.1 60.8 - - + -
162D LEU* 1.3 75.7 - - - +
164D GLN* 1.3 63.9 + - - +
165D VAL* 3.7 1.8 + - + +
173D ALA* 4.8 14.6 - - + -
174D THR 3.0 7.6 - - - +
175D GLU* 3.6 34.1 - - + -
176D VAL* 4.2 0.4 - - - -
189D PHE* 3.2 12.8 - - - -
190D ILE* 3.0 46.9 + - + +
192D ASP* 4.5 3.1 - - + -
216D VAL* 5.1 7.9 - - + -
220D ILE* 4.1 19.1 - - + -
224D GLU* 5.8 0.2 - - - -
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Residues in contact with GLN 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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163D PHE* 1.3 67.4 - - - +
165D VAL* 1.3 63.8 + - - +
166D LYS* 4.0 23.4 - - + +
172D ARG 3.0 2.6 - - - +
173D ALA* 3.0 4.5 - - - -
174D THR* 2.4 65.4 + - - +
176D VAL* 4.1 16.4 - - + +
182D SER 5.3 2.1 + - - +
184D ASN* 3.4 17.2 - - - +
187D ASP* 3.1 24.3 + - + +
188D CYS 4.6 0.2 - - - +
189D PHE* 3.7 24.9 - - + -
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Residues in contact with VAL 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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163D PHE* 4.3 5.6 - - + +
164D GLN* 1.3 77.4 - - - +
166D LYS* 1.3 58.5 + - - +
171D VAL* 3.5 20.2 - - + -
172D ARG 3.3 4.0 - - - +
173D ALA* 4.3 12.1 - - + -
187D ASP* 3.5 2.6 - - - +
188D CYS* 2.7 45.0 + - + +
190D ILE* 4.0 29.4 - - + -
209D GLU* 3.5 30.6 - - - +
212D LYS* 3.9 12.8 - - + -
213D ALA* 3.9 5.4 - - + +
216D VAL* 4.7 0.9 - - + -
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Residues in contact with LYS 166 (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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164D GLN* 3.8 19.9 - - + +
165D VAL* 1.3 73.4 - - - +
167D GLY* 1.3 59.0 + - - +
170D VAL 4.2 0.3 - - - +
171D VAL* 3.8 4.3 - - - -
172D ARG* 2.9 36.3 + - + +
174D THR* 6.0 0.2 - - - +
187D ASP* 3.2 27.1 + - - +
209D GLU* 3.4 4.3 - - - -
257D THR* 2.9 41.5 + - - +
258D GLU 3.3 13.2 - - - -
259D ASP* 2.6 30.9 + - - +
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Residues in contact with GLY 167 (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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166D LYS* 1.3 79.1 - - - +
168D ARG* 1.3 57.3 + - - -
170D VAL 3.7 10.1 - - - -
171D VAL* 4.1 8.5 - - - +
206D ASN* 2.8 31.4 + - - +
209D GLU* 2.6 18.6 + - - +
259D ASP* 3.8 17.0 - - - -
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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