Contacts of the helix formed by residues 1094 - 1108 (chain A) in PDB entry 4YC4
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 ASP1094 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1092A SER 3.9 1.6 + - - -
1093A LEU* 1.3 74.3 - - - +
1095A ALA* 1.3 67.2 + - - +
1096A VAL* 2.9 14.7 + - - +
1097A ARG* 2.7 61.7 + - - +
1098A ARG* 3.0 19.0 + - - +
1126A LYS* 4.5 11.4 + - - +
1158A GLY* 4.3 3.6 - - - +
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Residues in contact with ALA1095 (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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1001A GLY* 4.1 10.1 - - - -
1002A THR* 2.8 46.9 + - - +
1094A ASP* 1.3 73.1 - - - +
1096A VAL* 1.3 64.3 + - + +
1098A ARG* 3.6 8.7 - - - +
1099A ALA* 3.4 11.4 + - - +
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Residues in contact with VAL1096 (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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170A LEU* 4.7 8.7 - - + -
1001A GLY* 5.3 3.1 - - - +
1094A ASP* 3.1 7.3 + - - +
1095A ALA* 1.3 80.2 - - + +
1097A ARG* 1.3 66.2 + - - +
1099A ALA* 3.2 17.5 + - - +
1100A ALA 3.2 4.2 + - - -
1154A THR* 3.6 27.7 - - + +
1158A GLY 3.6 32.3 - - - +
1159A THR* 3.9 7.6 - - - +
1160A TRP* 3.5 37.7 - - + +
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Residues in contact with ARG1097 (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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1093A LEU* 3.8 18.2 - - + +
1094A ASP* 2.7 47.5 + - - +
1096A VAL* 1.3 72.9 - - - +
1098A ARG* 1.3 57.5 + - - +
1100A ALA* 2.7 24.5 + - - +
1101A LEU 3.0 9.5 + - - -
1128A TRP* 2.9 68.4 - - - +
1154A THR 4.0 7.0 - - - +
1155A PHE* 2.6 43.6 + - + +
1156A ARG 3.1 15.6 + - - -
1157A THR 3.7 1.6 - - - -
1158A GLY* 3.2 22.0 - - - +
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Residues in contact with ARG1098 (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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1002A THR* 4.0 13.0 + - + +
1090A TYR* 2.9 55.6 + - + +
1091A ASP* 2.8 38.7 + - - +
1093A LEU* 3.1 23.3 + - + +
1094A ASP 3.0 17.5 + - - +
1095A ALA* 3.6 12.8 - - - +
1097A ARG* 1.3 75.7 - - - +
1099A ALA* 1.3 62.4 + - - +
1101A LEU* 3.0 3.8 + - - +
1102A ILE* 3.0 28.4 + - - +
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Residues in contact with ALA1099 (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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1002A THR* 3.9 20.1 - - + +
1005A ILE* 3.0 36.3 - - + +
1008A MET* 3.9 3.1 - - - +
1095A ALA 3.4 9.4 + - - +
1096A VAL 3.2 11.8 + - - +
1097A ARG 3.1 0.6 - - - -
1098A ARG* 1.3 77.5 - - - +
1100A ALA* 1.3 57.5 + - - +
1102A ILE* 3.9 1.1 - - - -
1103A ASN* 3.0 12.5 + - - +
1160A TRP* 3.6 27.4 - - + -
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Residues in contact with ALA1100 (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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1008A MET* 4.3 4.7 - - - -
1096A VAL 3.2 3.4 + - - +
1097A ARG* 2.7 21.8 + - - +
1099A ALA* 1.3 72.3 - - - +
1101A LEU* 1.3 62.5 + - - -
1103A ASN* 3.1 17.5 + - - +
1104A MET* 3.2 17.0 + - - +
1151A VAL* 3.8 12.4 - - + +
1154A THR* 4.3 14.8 - - + -
1155A PHE* 3.2 31.6 - - + -
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Residues in contact with LEU1101 (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 16.4 - - + -
1086A LEU* 4.3 18.6 - - + +
1089A VAL* 4.9 4.3 - - + -
1090A TYR* 4.0 36.6 - - + +
1093A LEU* 4.4 9.2 - - + -
1097A ARG 3.0 8.1 + - - +
1098A ARG 3.0 6.5 + - - +
1100A ALA* 1.3 76.5 - - - +
1102A ILE* 1.3 62.9 + - - +
1104A MET* 3.1 18.6 + - - +
1105A VAL* 3.1 13.4 + - + +
1113A VAL* 4.0 27.1 - - + -
1120A LEU* 5.2 7.0 - - + -
1123A LEU* 4.7 10.5 - - + -
1155A PHE* 3.3 17.9 - - + -
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Residues in contact with ILE1102 (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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1002A THR* 3.7 30.7 - - + -
1005A ILE* 3.6 23.8 - - + -
1009A LEU* 5.3 3.4 - - + -
1073A VAL* 4.9 5.2 - - + -
1076A ALA* 4.0 19.4 - - + +
1077A VAL* 4.1 21.5 - - + -
1080A ILE* 3.6 20.2 - - + +
1090A TYR* 3.8 16.8 - - + +
1098A ARG 3.0 11.4 + - - +
1099A ALA* 3.7 6.7 - - - +
1101A LEU* 1.3 77.1 - - - +
1103A ASN* 1.3 63.4 + - - +
1105A VAL* 3.1 2.9 + - - +
1106A PHE* 2.8 21.5 + - - +
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Residues in contact with ASN1103 (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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1005A ILE* 3.7 2.9 - - + +
1008A MET* 3.4 33.3 + - + +
1009A LEU* 3.6 21.2 - - - +
1012A ASP* 3.2 21.5 + - - -
1099A ALA 3.0 15.8 + - - +
1100A ALA 3.1 12.3 + - - +
1102A ILE* 1.3 74.6 - - - +
1104A MET* 1.3 63.4 + - - +
1106A PHE* 3.2 5.1 + - - +
1107A GLN* 3.1 16.5 + - - +
1140A TRP* 6.0 0.2 - - - -
1147A ARG* 2.5 37.7 + - - -
1151A VAL* 3.9 12.1 - - + +
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Residues in contact with MET1104 (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 ALA 3.3 13.9 - - - +
1101A LEU* 3.1 10.2 + - - +
1103A ASN* 1.3 77.4 - - - +
1105A VAL* 1.3 53.6 + - - +
1106A PHE 3.0 0.2 - - - -
1107A GLN* 3.0 7.0 + - - +
1108A MET* 2.6 57.7 + - + +
1113A VAL* 3.6 26.5 - - + -
1116A PHE* 4.3 15.3 - - + -
1123A LEU* 6.2 0.2 - - - -
1135A LEU* 4.9 5.2 - - + -
1140A TRP* 3.3 39.9 - - + -
1151A VAL* 4.2 11.7 - - + -
1155A PHE* 3.6 26.0 - - - -
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Residues in contact with VAL1105 (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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1076A ALA* 3.5 35.5 - - - +
1079A GLY* 4.8 2.2 - - - -
1080A ILE* 3.8 22.0 - - + -
1086A LEU* 3.8 11.7 - - + -
1101A LEU* 3.1 12.0 + - + +
1102A ILE 3.1 4.5 + - - +
1104A MET* 1.3 75.1 - - - +
1106A PHE* 1.3 59.7 + - - +
1109A GLY* 3.0 24.1 + - - +
1110A GLU* 3.7 17.3 - - - +
1113A VAL* 3.4 30.7 - - + -
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Residues in contact with PHE1106 (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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1009A LEU* 3.4 38.4 - - + -
1013A GLU* 4.0 22.4 - - + -
1031A ILE 3.6 24.0 - - - -
1032A GLY* 4.0 17.1 - - - +
1069A PHE* 3.9 18.6 - + - -
1072A ASP* 3.7 43.5 - - + -
1073A VAL* 4.1 5.2 - - + -
1076A ALA* 4.3 7.9 - - + -
1102A ILE* 2.8 12.0 + - + +
1103A ASN 3.2 11.0 - - - +
1105A VAL* 1.3 80.2 - - - +
1107A GLN* 1.3 63.2 + - - +
1109A GLY 4.5 0.7 + - - -
1147A ARG* 4.5 0.2 - - - -
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Residues in contact with GLN1107 (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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1013A GLU* 4.9 2.7 + - - +
1103A ASN 3.1 8.0 + - - +
1104A MET* 3.0 7.5 + - - +
1106A PHE* 1.3 86.6 - - - +
1108A MET* 1.3 65.9 + - + +
1109A GLY 3.6 0.2 - - - -
1140A TRP* 2.5 37.7 + - - -
1144A THR* 3.5 22.2 + - - +
1147A ARG* 3.3 44.6 + - - +
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Residues in contact with MET1108 (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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1104A MET* 2.6 61.9 + - + +
1107A GLN* 1.3 82.8 - - + +
1109A GLY* 1.3 61.5 + - - +
1112A GLY* 4.0 13.1 + - - -
1113A VAL* 3.9 14.4 - - + +
1116A PHE* 4.0 16.4 - - + -
1140A TRP* 3.8 40.6 - - + +
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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