Contacts of the helix formed by residues 1126 - 1134 (chain A) in PDB entry 1YA6
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 GLY1126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1083A VAL* 5.1 0.2 - - - -
1093A ILE* 3.5 14.3 - - - +
1096A TYR* 3.7 10.7 - - - -
1097A LYS* 4.1 8.9 - - - +
1125A LEU* 1.3 73.8 - - - +
1127A LEU* 1.3 55.6 + - - +
1128A GLU 3.4 1.8 - - - -
1129A GLU* 3.4 23.2 + - - +
1130A THR* 2.5 33.9 + - - -
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Residues in contact with LEU1127 (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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1083A VAL* 4.6 19.5 - - + -
1111A VAL* 5.7 6.3 - - + -
1113A GLN* 4.3 13.7 - - - +
1121A LEU* 4.0 36.1 - - + +
1124A ASN* 3.8 31.9 - - + +
1125A LEU* 3.0 3.1 - - - +
1126A GLY* 1.3 76.4 - - - +
1128A GLU* 1.3 66.1 + - - +
1130A THR* 3.3 8.2 + - + +
1131A VAL* 3.1 39.2 + - + +
1146A PHE* 4.6 11.2 - - + -
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Residues in contact with GLU1128 (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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1126A GLY 3.4 0.2 - - - -
1127A LEU* 1.3 79.7 - - - +
1129A GLU* 1.3 66.1 + - - +
1131A VAL* 3.5 7.9 + - + +
1132A ARG* 2.8 68.3 + - + +
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Residues in contact with GLU1129 (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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1097A LYS* 3.0 46.0 + - + +
1100A LEU* 3.3 26.2 - - + +
1126A GLY* 3.4 17.8 - - - +
1127A LEU 3.3 0.2 - - - -
1128A GLU* 1.3 82.1 + - - +
1130A THR* 1.3 64.5 - - - +
1132A ARG* 3.5 12.7 + - - +
1133A ARG* 3.4 19.4 + - - +
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Residues in contact with THR1130 (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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1080A ILE* 3.9 17.9 - - + -
1083A VAL* 3.8 6.6 - - + +
1096A TYR* 3.0 26.3 + - - +
1100A LEU* 3.4 9.2 - - + +
1109A VAL* 5.2 0.9 - - + +
1111A VAL* 3.6 31.8 - - + +
1126A GLY 2.5 24.7 + - - -
1127A LEU* 3.5 12.4 + - - -
1128A GLU 3.3 0.2 - - - -
1129A GLU* 1.3 78.9 - - - +
1131A VAL* 1.3 58.3 + - - +
1133A ARG* 3.3 2.8 + - - +
1134A ALA* 2.9 28.9 + - - +
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Residues in contact with VAL1131 (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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1111A VAL* 5.5 5.8 - - + -
1127A LEU* 3.1 25.1 + - + +
1128A GLU* 3.8 9.9 - - + +
1129A GLU 3.3 0.2 - - - -
1130A THR* 1.3 78.8 - - - +
1132A ARG* 1.3 61.3 + - + +
1133A ARG 3.5 0.5 + - - -
1134A ALA* 3.5 19.1 + - - +
1137A ILE* 3.7 26.0 - - + +
1146A PHE* 4.3 20.6 - - + -
1169A PRO* 5.1 6.8 - - - +
2003A NCO 5.5 1.4 + - - -
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Residues in contact with ARG1132 (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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1128A GLU* 2.8 54.6 + - + +
1129A GLU* 3.9 12.0 - - - +
1130A THR 3.3 0.6 - - - -
1131A VAL* 1.3 78.4 - - + +
1133A ARG* 1.3 58.0 + - - +
2003A NCO 3.0 29.2 + - - -
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Residues in contact with ARG1133 (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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1100A LEU* 3.7 30.4 + - + +
1103A ILE* 3.5 29.0 + - + +
1104A LYS 3.0 22.4 + - - -
1105A PRO* 4.1 9.6 + - - +
1107A ILE 2.9 22.0 + - - -
1109A VAL* 3.5 19.2 - - + +
1129A GLU 3.4 12.8 + - - +
1130A THR 3.3 3.8 + - - +
1131A VAL 3.3 0.2 - - - -
1132A ARG* 1.3 77.5 - - - +
1134A ALA* 1.3 66.1 + - - +
1135A ASP* 3.1 24.4 + - - -
2003A NCO 3.5 10.9 + - - -
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Residues in contact with ALA1134 (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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1109A VAL* 3.6 10.3 - - - +
1111A VAL* 3.3 28.9 - - + -
1130A THR 2.9 10.6 + - - +
1131A VAL* 3.8 7.8 - - - +
1132A ARG 3.5 1.2 - - - -
1133A ARG* 1.3 79.8 - - - +
1135A ASP* 1.3 60.6 + - - +
1136A VAL 3.9 2.9 - - - +
1137A ILE* 3.7 25.6 - - + -
1169A PRO* 4.1 7.6 - - - +
2003A NCO 3.4 18.9 + - - -
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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