Contacts of the strand formed by residues 1166 - 1171 (chain A) in PDB entry 3Q71
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 GLU1166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014A LEU* 3.8 0.8 - - - +
1015A GLN* 3.3 23.6 - - - +
1017A LEU* 4.0 6.3 - - + +
1125A LYS* 3.1 25.7 + - - +
1126A SER* 3.2 17.5 - - - -
1127A ILE 3.0 23.0 + - - -
1164A LEU* 3.8 5.8 - - - +
1165A GLN* 1.3 87.4 - - + +
1167A VAL* 1.3 64.1 + - - +
1168A HIS* 2.7 39.8 + - + +
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Residues in contact with VAL1167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014A LEU* 4.1 17.7 - - + -
1015A GLN 2.8 11.6 + - - +
1016A MET* 3.2 10.9 - - + +
1017A LEU* 3.0 23.7 + - - +
1116A MET* 4.2 8.5 - - + -
1127A ILE* 3.3 13.5 - - + +
1129A PHE* 3.6 33.4 - - + -
1152A VAL* 4.1 24.5 - - + -
1164A LEU* 4.9 2.2 - - + -
1166A GLU* 1.3 76.7 - - - +
1168A HIS* 1.3 64.8 + - - +
1169A PHE* 3.9 19.3 + - + -
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Residues in contact with HIS1168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017A LEU* 3.5 25.9 - - + +
1019A VAL* 4.0 17.2 - - + +
1021A GLU* 5.6 1.6 + - - -
1027A LYS 6.2 0.7 - - - -
1028A THR* 3.5 27.5 - - + +
1126A SER* 4.5 0.6 - - - -
1127A ILE 2.8 13.6 + - - +
1128A ALA* 3.2 4.3 - - + -
1129A PHE* 2.8 27.9 + - - +
1166A GLU* 2.7 39.0 + - + +
1167A VAL* 1.3 78.7 - - - +
1169A PHE* 1.3 63.3 + - - +
1170A LEU* 3.7 18.1 + - + +
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Residues in contact with PHE1169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016A MET* 3.9 27.4 - - + -
1017A LEU 2.8 20.3 + - - +
1018A LEU* 4.1 4.2 - - + -
1019A VAL 3.0 27.2 + - - +
1129A PHE* 3.3 7.9 - - + +
1148A ILE* 3.7 34.3 - - + -
1149A ILE* 3.8 27.8 - - + -
1152A VAL* 4.1 11.7 - - + -
1167A VAL* 3.9 15.0 - - + -
1168A HIS* 1.3 74.6 - - - +
1170A LEU* 1.3 61.7 + - - +
1171A LEU* 3.6 6.1 + - + +
1182A PHE* 3.6 31.9 - + + -
1186A PHE* 3.9 23.3 - + - -
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Residues in contact with LEU1170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A AR6 4.4 3.6 + - + -
1019A VAL* 3.6 14.1 - - + -
1021A GLU* 3.8 29.4 - - + +
1023A VAL* 3.8 24.2 - - + -
1026A ALA* 3.4 31.9 - - + -
1028A THR* 5.8 0.2 - - + -
1128A ALA* 3.7 16.6 - - + -
1129A PHE 2.9 13.0 + - - +
1130A PRO* 3.3 28.3 - - + +
1131A ALA 3.9 2.1 + - - -
1168A HIS* 3.7 28.0 - - + +
1169A PHE* 1.3 72.3 - - - +
1171A LEU* 1.3 65.3 - - - +
1172A HIS 4.1 1.2 + - - -
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Residues in contact with LEU1171 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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993A LEU* 4.1 17.9 - - + -
1018A LEU* 4.4 8.7 - - + -
1019A VAL 2.8 15.5 + - - +
1020A LYS* 3.3 6.1 - - - +
1021A GLU 2.9 25.3 + - - -
1130A PRO 5.9 0.4 - - - -
1131A ALA* 4.7 6.1 - - + +
1169A PHE 4.0 6.5 - - - +
1170A LEU* 1.3 80.7 - - - +
1172A HIS* 1.3 63.8 + - - +
1175A ASP 5.4 0.2 - - - +
1178A ASN* 4.0 15.3 - - + -
1179A ILE* 3.9 31.9 - - + +
1182A PHE* 3.6 56.3 - - + -
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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