Contacts of the helix formed by residues 1120 - 1128 (chain A) in PDB entry 5B16
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 HIS1120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1086A LEU 3.2 24.2 - - - +
1087A GLN* 3.5 34.9 + - + +
1090A GLU* 2.5 30.1 + - + +
1091A PRO 4.2 3.8 - - - -
1092A ASN 3.2 26.0 - - - -
1093A THR* 3.9 0.8 - - - -
1094A ASP* 3.3 26.0 - - - +
1118A PHE* 3.9 5.4 - - - -
1119A THR* 1.3 81.3 - - + +
1121A VAL* 1.3 62.0 + - - +
1122A ARG* 3.1 6.1 + - + +
1123A LEU* 3.2 22.1 + - + +
1231A ASP* 2.7 19.4 + - - +
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Residues in contact with VAL1121 (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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1094A ASP* 3.3 14.2 + - + -
1095A ARG* 3.2 30.5 - - - +
1098A ILE* 4.3 3.6 - - + -
1104A LEU* 3.7 40.8 - - + +
1107A LEU* 4.4 16.4 - - + -
1111A GLU* 3.6 21.5 - - - +
1118A PHE* 4.5 5.8 - - - +
1119A THR 4.3 1.3 - - - +
1120A HIS* 1.3 69.3 - - - +
1122A ARG* 1.3 58.6 + - - +
1123A LEU 3.1 0.4 - - - -
1124A LEU* 3.3 8.9 + - + +
1125A ALA* 2.9 29.0 + - - +
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Residues in contact with ARG1122 (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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1086A LEU* 3.4 55.9 - - + +
1089A GLN* 4.0 21.8 + - - +
1090A GLU* 4.9 10.7 + - - +
1094A ASP* 3.3 23.8 + - + +
1097A LEU* 3.4 28.0 - - + +
1104A LEU* 5.9 5.2 - - + -
1120A HIS 3.1 0.8 - - - +
1121A VAL* 1.3 78.6 - - - +
1123A LEU* 1.3 56.6 + - + +
1125A ALA* 4.2 3.6 - - - -
1126A ARG* 2.9 27.9 + - - +
1137A HIS* 2.7 54.4 + - - -
1138A LEU* 3.5 22.7 + - + +
1139A THR* 3.5 4.2 + - - -
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Residues in contact with LEU1123 (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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1084A HIS* 3.4 40.4 - - + +
1086A LEU* 4.1 7.9 - - + -
1087A GLN* 3.4 33.0 - - + +
1118A PHE* 4.8 1.6 - - + -
1120A HIS* 3.6 18.4 - - + +
1121A VAL 3.1 0.2 - - - -
1122A ARG* 1.3 75.3 - - - +
1124A LEU* 1.3 61.0 + - - +
1126A ARG* 3.0 6.0 + - - +
1127A ALA* 2.9 27.5 + - - +
1146A MET* 3.8 19.9 - - + +
1227A ALA* 3.7 14.0 - - + +
1230A ILE* 3.6 16.8 - - + -
1231A ASP* 3.9 15.3 - - + +
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Residues in contact with LEU1124 (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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1107A LEU* 3.8 21.3 - - + -
1110A PHE* 4.2 12.3 - - + -
1111A GLU* 4.2 20.0 - - + +
1118A PHE* 3.6 40.7 - - + -
1120A HIS 4.1 0.6 + - - -
1121A VAL* 3.3 10.1 + - + +
1123A LEU* 1.3 78.0 - - - +
1125A ALA* 1.3 62.5 + - - +
1127A ALA* 3.3 11.4 + - + +
1128A PHE* 3.4 29.7 + - + -
1224A PHE* 3.6 34.1 - - + -
1227A ALA* 4.2 7.3 - - + +
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Residues in contact with ALA1125 (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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1103A VAL* 5.5 2.2 - - + -
1104A LEU* 4.6 13.0 - - + -
1107A LEU* 3.7 19.4 - - + +
1121A VAL 2.9 17.8 + - - +
1122A ARG* 3.7 4.7 - - - +
1124A LEU* 1.3 75.1 - - - +
1126A ARG* 1.3 56.0 + - - +
1128A PHE* 3.5 1.8 + - - -
1129A THR* 2.6 29.5 + - - -
1138A LEU* 5.0 5.6 - - + +
1139A THR* 3.6 14.1 - - - +
1201A ILE* 3.5 16.6 - - + +
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Residues in contact with ARG1126 (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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985A TYR* 4.5 0.4 + - - -
1084A HIS* 4.4 10.7 + - - -
1086A LEU* 4.4 11.4 - - + +
1122A ARG 2.9 15.8 + - - +
1123A LEU* 3.0 9.4 + - - +
1125A ALA* 1.3 75.4 - - - +
1127A ALA* 1.3 60.0 + - - +
1128A PHE 3.1 0.2 - - - -
1129A THR* 3.0 19.6 + - - -
1139A THR* 3.5 21.3 + - + -
1140A LEU* 2.2 41.2 + - - +
1141A GLY* 4.0 2.0 - - - -
1142A HIS* 3.0 31.1 + - - +
1143A ASN* 3.1 13.0 - - - +
1145A ARG* 3.0 44.7 - - - +
1146A MET* 3.6 32.7 - - - +
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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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1123A LEU 2.9 12.7 + - - +
1124A LEU* 3.3 12.1 + - + +
1126A ARG* 1.3 75.5 - - - +
1128A PHE* 1.3 66.1 + - + +
1143A ASN* 2.9 26.8 - - - +
1146A MET* 4.0 2.9 - - - -
1220A LEU* 3.9 6.2 - - - +
1223A SER* 3.3 38.6 - - - +
1224A PHE* 3.9 5.8 - - - +
1227A ALA* 3.8 9.2 - - + -
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Residues in contact with PHE1128 (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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1107A LEU* 4.3 13.0 - - + -
1110A PHE* 3.4 41.5 - + - -
1124A LEU* 3.4 34.8 + - + +
1125A ALA 3.5 4.7 + - - +
1126A ARG 3.1 0.6 - - - -
1127A ALA* 1.3 83.7 - - - +
1129A THR* 1.3 57.3 + - - +
1130A LEU* 3.4 6.3 + - - +
1143A ASN* 3.7 1.3 - - - -
1196A MET* 4.3 17.9 - - + -
1199A TYR* 3.3 39.9 - - + +
1200A ALA* 3.6 3.3 - - - -
1201A ILE* 2.7 37.2 + - + -
1220A LEU* 4.2 19.1 - - + -
1224A PHE* 4.2 18.8 - + + -
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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