Contacts of the helix formed by residues 164 - 171 (chain D) in PDB entry 3S7K
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 GLU 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D ALA* 3.4 28.7 - - + +
163D VAL* 1.3 77.2 - - - +
165D ARG* 1.3 66.9 + - - +
166D PRO* 4.1 11.4 - - + +
167D VAL* 3.0 25.8 + - + -
168D CYS* 3.1 9.5 + - - -
401D TRS 4.2 3.1 - - - -
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Residues in contact with ARG 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 VAL 3.5 1.8 + - - -
164D GLU* 1.3 72.6 + - - +
166D PRO* 1.4 65.6 - - + +
168D CYS* 3.1 5.2 + - - +
169D LYS* 2.9 29.6 + - + +
176D ILE* 4.0 22.1 - - + +
177D THR 3.0 21.8 + - - -
178D ASP* 4.1 26.8 + - - +
180D MET 2.7 30.1 + - - -
181D PHE* 4.1 0.4 - - - +
230D HIS* 4.8 1.6 - - - -
401D TRS 2.9 60.3 + - - -
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Residues in contact with PRO 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D GLU* 3.5 15.0 - - + +
165D ARG* 1.4 93.5 - - + +
167D VAL* 1.3 58.3 + - + +
169D LYS* 3.8 8.5 - - + +
170D ASP* 3.1 36.5 + - - +
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Residues in contact with VAL 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D VAL* 3.6 18.6 - - + -
164D GLU* 3.0 20.5 + - + +
166D PRO* 1.3 76.5 - - + +
168D CYS* 1.3 66.4 + - - +
170D ASP* 3.3 7.4 + - + +
171D SER* 3.1 24.3 + - - -
225D PRO* 5.8 2.0 - - + -
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Residues in contact with CYS 168 (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 VAL* 3.5 10.7 - - - +
164D GLU 3.1 9.0 + - - -
165D ARG* 3.4 7.4 - - - +
167D VAL* 1.3 76.4 - - - +
169D LYS* 1.3 61.7 + - - +
171D SER* 2.7 24.2 + - - -
172D THR* 3.7 9.4 - - - +
176D ILE* 4.1 9.2 - - + -
181D PHE* 4.7 0.4 - - - -
182D CYS* 2.0 53.8 - - + -
227D PHE* 3.7 11.0 - - + -
401D TRS 3.3 25.8 - - - -
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Residues in contact with LYS 169 (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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165D ARG* 2.9 19.1 + - + +
166D PRO* 3.8 9.4 - - + +
167D VAL 3.3 0.2 - - - -
168D CYS* 1.3 76.4 - - - +
170D ASP* 1.3 63.8 + - - +
172D THR* 2.9 27.2 - - - +
173D ARG* 4.5 1.4 + - - -
174D ILE 5.2 0.9 - - - +
176D ILE* 3.8 25.7 - - + +
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Residues in contact with ASP 170 (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 PRO* 3.1 24.2 + - - +
167D VAL* 3.8 7.9 - - + +
168D CYS 3.2 0.2 - - - -
169D LYS* 1.3 84.3 + - - +
171D SER* 1.3 60.6 + - - +
172D THR 3.2 0.9 - - - -
173D ARG* 3.4 19.5 + - - +
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Residues in contact with SER 171 (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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167D VAL* 3.1 14.5 + - - -
168D CYS 2.7 18.6 + - - -
170D ASP* 1.3 77.0 - - - +
172D THR* 1.3 59.3 + - - +
173D ARG* 4.9 0.7 - - - -
217D GLU* 5.2 0.2 - - - +
223D GLY 3.5 21.3 - - - -
224D LYS* 2.9 32.3 + - - +
225D PRO* 3.8 22.9 - - - +
227D PHE* 3.9 10.0 - - - -
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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