Contacts of the helix formed by residues 1124 - 1131 (chain A) in PDB entry 4Z4Q
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 SER1124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055A PHE* 3.6 2.8 + - - +
1097A ILE* 2.8 30.7 + - - -
1098A LEU* 2.9 18.5 + - - -
1099A VAL* 4.2 1.1 - - - +
1100A GLU* 3.7 24.5 - - - -
1122A ARG 3.7 1.2 + - - -
1123A LEU* 1.3 79.5 - - - +
1125A GLU* 1.3 65.3 + - - +
1126A ILE* 3.7 4.0 - - - +
1127A ALA* 3.1 26.3 + - - +
1128A GLY 3.4 3.3 + - - -
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Residues in contact with GLU1125 (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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1055A PHE* 3.3 58.8 - - + +
1100A GLU* 4.3 4.4 + - - +
1124A SER* 1.3 72.4 - - - +
1126A ILE* 1.3 58.5 + - - +
1128A GLY* 2.8 22.6 + - - -
1129A TYR* 3.8 9.7 + - + -
1473A LYS* 2.8 34.7 + - - +
1474A PHE* 4.2 14.2 - - + -
549B LYS 5.1 0.2 - - - +
550B GLY* 5.7 0.7 - - - -
551B LYS* 4.3 18.7 + - - +
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Residues in contact with ILE1126 (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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1096A GLU* 3.4 32.8 - - + -
1097A ILE 4.0 7.0 - - - +
1098A LEU* 3.9 18.2 - - + -
1124A SER* 3.3 11.6 + - - +
1125A GLU* 1.3 78.4 - - - +
1127A ALA* 1.3 57.7 + - - +
1129A TYR* 2.6 31.8 + - + +
1130A LEU 3.6 2.9 + - - -
1159A PHE* 3.8 28.6 - - + -
1183A LEU* 4.6 7.0 - - + -
1474A PHE* 3.6 51.6 - - + -
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Residues in contact with ALA1127 (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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1045A LEU* 4.4 11.2 - - + +
1098A LEU* 3.3 41.3 - - + +
1123A LEU* 4.1 10.8 - - + -
1124A SER* 3.1 15.3 + - - +
1126A ILE* 1.3 84.3 - - - +
1128A GLY* 1.3 62.6 + - - +
1129A TYR 3.1 0.3 + - - -
1130A LEU* 3.1 18.0 + - - +
1131A LEU* 3.5 15.4 + - - +
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Residues in contact with GLY1128 (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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1049A ASN* 5.6 3.4 - - - -
1055A PHE* 6.3 1.3 - - - -
1123A LEU* 5.4 2.1 - - - +
1124A SER 3.4 4.5 + - - -
1125A GLU 2.8 14.1 + - - -
1127A ALA* 1.3 78.2 - - - +
1129A TYR* 1.3 63.2 + - - +
1131A LEU* 3.1 11.5 + - - +
1132A GLN* 3.1 21.3 + - - +
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Residues in contact with TYR1129 (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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1125A GLU* 3.8 12.3 - - + -
1126A ILE* 2.6 17.2 + - - +
1128A GLY* 1.3 71.2 - - - -
1130A LEU* 1.3 61.6 + - - +
1131A LEU 3.1 1.0 + - - -
1132A GLN* 3.2 37.7 + - - +
1156A PRO* 5.1 0.2 - - - +
1157A ALA 4.4 0.3 + - - -
1158A ALA* 3.4 30.9 + - + +
1159A PHE* 4.3 12.1 - - + -
1470A VAL* 3.8 28.5 - - + -
1473A LYS* 3.5 27.1 + - + +
1474A PHE* 3.4 37.0 - + + -
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Residues in contact with LEU1130 (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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1035A ASP* 4.5 6.5 - - + +
1037A LEU* 4.2 11.0 - - + -
1045A LEU* 3.7 24.7 - - + -
1098A LEU* 4.0 25.8 - - + -
1126A ILE 3.6 1.6 + - - -
1127A ALA* 3.1 10.6 + - - +
1129A TYR* 1.3 76.0 - - - +
1131A LEU* 1.3 58.1 + - + +
1155A LEU* 3.3 23.8 - - + +
1156A PRO* 3.4 3.5 - - - +
1157A ALA* 3.1 41.7 + - + +
1159A PHE* 3.7 22.1 - - + +
1161A ASN* 3.8 29.2 - - + -
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Residues in contact with LEU1131 (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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1045A LEU* 4.0 8.5 - - + +
1046A TYR* 4.3 13.7 - - + +
1049A ASN* 3.3 51.6 - - + +
1123A LEU* 3.6 17.3 - - + -
1127A ALA 3.8 12.8 - - - +
1128A GLY* 3.1 8.5 + - - +
1129A TYR 3.1 1.0 - - - -
1130A LEU* 1.3 77.3 - - + +
1132A GLN* 1.3 67.3 + - - +
1133A ASP 3.0 3.8 + - - -
1134A ILE* 3.0 29.2 + - + +
1135A GLU* 4.5 0.5 - - - +
1155A LEU* 3.9 34.3 - - + -
1156A PRO* 4.1 4.3 - - - -
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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