Contacts of the helix formed by residues 167 - 176 (chain D) in PDB entry 6R7H
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 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D VAL* 3.3 46.7 - - + +
148D TYR* 3.9 27.5 - + + +
151D ILE* 3.7 35.2 - - + -
152D ALA* 5.2 2.0 - - - +
155D TYR* 4.4 7.6 - + - -
163D GLN* 3.9 18.0 + - + +
164D ALA 4.1 2.2 + - - +
166D ALA* 1.3 81.2 - - + +
168D ILE* 1.3 61.7 + - - +
169D ASN 3.3 1.9 + - - -
170D ARG* 3.5 63.4 + - - +
171D ALA 4.1 2.1 + - - -
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Residues in contact with ILE 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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148D TYR 5.3 2.0 - - - +
149D LEU* 5.8 9.6 - - + -
152D ALA* 4.4 14.5 - - + +
164D ALA 3.9 10.4 + - - +
165D GLU* 3.4 48.2 - - - +
167D TYR* 1.3 76.6 - - - +
169D ASN* 1.3 64.6 + - - +
170D ARG 3.2 0.2 - - - -
171D ALA* 3.4 17.8 + - + +
172D SER* 3.6 10.2 + - - -
186D HIS 5.7 0.7 - - - +
187D TYR* 4.8 19.0 - - + -
190D CYS* 5.5 8.7 - - + -
191D TYR* 3.7 9.9 - - + +
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Residues in contact with ASN 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ALA 3.7 1.7 + - - +
167D TYR 3.3 0.8 - - - -
168D ILE* 1.3 80.5 - - - +
170D ARG* 1.3 63.1 + - - +
172D SER* 3.3 16.9 + - - -
173D LEU* 4.1 12.5 + - - +
187D TYR* 3.0 27.4 + - - -
191D TYR* 3.1 26.0 + - - +
75R CYS* 3.1 24.4 + - - +
76R ASN* 3.9 21.3 - - + +
99R ARG* 3.9 7.5 - - - +
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Residues in contact with ARG 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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132D LEU* 5.9 1.8 - - - +
133D GLU* 4.1 22.8 - - - +
148D TYR* 3.6 45.1 + - + +
166D ALA 4.7 4.0 - - - +
167D TYR* 3.5 47.6 + - - +
168D ILE 3.2 0.8 - - - -
169D ASN* 1.3 80.1 - - + +
171D ALA* 1.3 59.9 + - - +
172D SER 3.5 0.3 + - - -
173D LEU* 3.6 23.4 + - - +
174D LEU* 4.5 6.1 + - - +
36R ASP* 3.4 33.1 + - - +
37R ILE* 5.0 13.4 - - + +
76R ASN* 4.4 20.8 - - + +
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Residues in contact with ALA 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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145D LEU* 3.8 26.7 - - + +
148D TYR* 3.8 30.4 - - + -
149D LEU* 6.2 0.7 - - + -
167D TYR 4.1 1.4 + - - -
168D ILE* 3.4 15.0 + - + +
169D ASN 3.3 0.4 - - - -
170D ARG* 1.3 76.3 - - - +
172D SER* 1.3 62.8 + - - +
173D LEU 3.2 1.5 + - - -
174D LEU* 3.5 6.6 + - - +
175D GLN* 3.3 25.1 + - - +
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Residues in contact with SER 172 (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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168D ILE 3.6 5.0 + - - -
169D ASN* 3.3 13.2 + - - -
170D ARG 3.2 1.4 - - - -
171D ALA* 1.3 76.9 - - - +
173D LEU* 1.3 65.9 + - - +
174D LEU 3.3 0.2 - - - -
175D GLN* 3.4 19.4 + - - +
176D ASN* 3.5 18.2 + - - +
184D GLN* 4.8 7.6 + - - +
187D TYR* 3.8 43.6 + - - -
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Residues in contact with LEU 173 (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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133D GLU* 5.8 1.3 - - - +
169D ASN* 4.3 11.4 - - - +
170D ARG* 3.9 15.7 - - - +
171D ALA 3.2 1.0 - - - -
172D SER* 1.3 80.6 - - - +
174D LEU* 1.3 63.2 + - + +
176D ASN* 3.4 22.4 + - - +
177D GLU* 4.9 4.5 - - - +
37R ILE* 4.8 25.6 - - + -
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Residues in contact with LEU 174 (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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138D GLN* 5.6 6.1 - - - +
141D VAL* 4.1 31.5 - - + +
144D LYS* 4.0 46.9 - - + +
145D LEU* 4.9 12.1 - - + +
148D TYR* 5.5 2.9 - - + -
170D ARG 4.5 7.6 + - - +
171D ALA* 3.5 9.6 + - - +
172D SER 3.3 0.2 - - - -
173D LEU* 1.3 79.2 - - + +
175D GLN* 1.3 62.8 + - - +
176D ASN 3.2 3.0 + - - -
177D GLU* 3.5 41.1 + - - +
178D SER* 4.0 6.9 + - - -
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Residues in contact with GLN 175 (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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145D LEU* 4.3 15.8 - - + +
171D ALA* 3.3 19.8 + - - +
172D SER* 3.7 14.0 + - - +
173D LEU 3.3 1.4 - - - -
174D LEU* 1.3 77.7 - - - +
176D ASN* 1.3 64.3 - - - +
177D GLU 3.2 0.2 - - - -
178D SER* 3.4 23.3 + - - +
180D ASN* 5.2 7.6 - - + +
183D LEU* 3.2 62.0 + - + +
184D GLN* 3.8 15.1 + - + +
187D TYR* 4.7 8.1 - - - +
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Residues in contact with ASN 176 (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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172D SER* 3.5 15.9 + - - +
173D LEU* 3.4 24.2 + - - +
174D LEU 3.2 1.0 - - - -
175D GLN* 1.3 78.7 - - - +
177D GLU* 1.3 61.1 + - + +
178D SER 3.5 7.6 + - - +
184D GLN* 4.1 13.6 - - - +
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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