Contacts of the helix formed by residues 1099 - 1110 (chain A) in PDB entry 4E5W
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 MET1099 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1096A HIS* 2.9 15.6 + - + +
1098A GLN* 1.4 80.8 - - + +
1100A THR* 1.3 63.8 + - - +
1101A VAL 3.4 1.8 - - - -
1102A THR* 3.1 32.5 + - - +
1103A ARG* 3.1 15.2 + - + +
1040B ASP* 3.2 51.4 - - + +
1043B SER* 4.5 5.4 - - - +
1045B VAL* 3.7 24.7 - - + -
1048B TYR* 6.0 1.3 - - + -
1052B CYS 4.6 4.3 - - - +
1053B LEU* 3.9 28.5 - - + +
1056B SER* 6.1 0.9 - - - +
1101B VAL* 4.0 18.6 - - + -
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Residues in contact with THR1100 (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 VAL* 5.8 0.9 - - + -
1046A PHE* 3.9 22.4 - - + -
1089A LEU* 4.2 11.3 - - + +
1092A ILE* 3.6 20.1 - - + +
1093A GLY 5.1 2.6 + - - +
1094A PRO 5.6 1.0 + - - -
1096A HIS* 3.7 12.3 + - - +
1097A GLY* 2.8 31.9 + - - -
1098A GLN 3.4 0.8 - - - -
1099A MET* 1.3 75.8 - - - +
1101A VAL* 1.4 60.9 - - + +
1103A ARG* 3.2 6.9 + - - +
1104A LEU* 2.9 27.4 + - + +
1098B GLN* 6.1 1.6 - - - +
1201B PEG 4.8 4.5 + - - -
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Residues in contact with VAL1101 (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 VAL* 3.9 30.1 - - + -
1053A LEU* 4.1 19.7 - - + -
1098A GLN 4.7 2.0 + - - +
1099A MET 3.4 0.6 - - - -
1100A THR* 1.4 74.6 - - - +
1102A THR* 1.4 61.3 + - - +
1104A LEU* 3.2 7.8 + - + +
1105A VAL* 2.9 27.2 + - - +
1098B GLN* 3.7 34.8 - - + +
1099B MET* 4.1 16.4 - - + -
1102B THR* 3.7 26.2 - - + +
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Residues in contact with THR1102 (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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1098A GLN 5.4 0.6 + - - -
1099A MET* 3.1 29.9 + - - +
1101A VAL* 1.4 76.1 - - - +
1103A ARG* 1.3 56.4 + - - +
1105A VAL* 3.4 6.9 + - + +
1106A ASN* 2.9 28.1 + - - +
1053B LEU 3.4 26.8 + - - +
1054B MET* 4.1 7.7 - - + +
1101B VAL* 3.7 21.7 - - + +
1102B THR* 3.5 27.4 - - + +
1105B VAL* 4.2 10.8 - - + -
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Residues in contact with ARG1103 (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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1092A ILE* 4.2 20.0 + - + -
1096A HIS* 3.1 40.1 + - + -
1099A MET* 3.1 16.8 + - + +
1100A THR* 3.5 9.2 - - - +
1102A THR* 1.3 75.1 - - - +
1104A LEU* 1.4 58.0 + - - +
1106A ASN* 3.4 6.4 + - - +
1107A THR* 2.9 34.4 + - - +
1037B VAL 2.8 32.3 + - - -
1038B LYS* 3.7 5.9 + - - +
1040B ASP* 2.7 30.4 + - - +
1054B MET 5.5 0.4 - - - -
1056B SER* 3.2 25.9 + - - +
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Residues in contact with LEU1104 (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 VAL* 3.7 33.2 - - + +
1046A PHE* 3.8 22.9 - - + -
1053A LEU* 3.8 18.2 - - + -
1088A PHE* 3.7 44.0 - - + -
1092A ILE* 4.0 14.3 - - + +
1100A THR 2.9 13.9 + - - +
1101A VAL* 3.2 11.6 + - - +
1103A ARG* 1.4 73.7 - - - +
1105A VAL* 1.4 59.4 + - - +
1107A THR* 3.4 3.3 + - - -
1108A LEU* 3.0 40.1 + - + +
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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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1050A PRO* 5.0 3.4 - - + +
1053A LEU* 3.6 32.3 - - + -
1054A MET* 3.6 36.1 - - + -
1101A VAL 2.9 19.4 + - - +
1102A THR* 3.7 8.7 - - + +
1104A LEU* 1.4 74.2 - - - +
1106A ASN* 1.4 58.5 + - - +
1108A LEU* 3.3 8.7 + - - +
1109A LYS* 2.9 43.1 + - + +
1134A PHE* 5.0 0.5 - - - -
1102B THR* 4.2 12.6 - - + -
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Residues in contact with ASN1106 (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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1102A THR 2.9 17.9 + - - +
1103A ARG* 3.7 7.6 - - - +
1105A VAL* 1.4 78.1 - - - +
1107A THR* 1.3 61.3 + - - +
1109A LYS* 3.4 15.9 + - - +
1110A GLU* 3.1 50.0 + - - +
1054B MET* 3.5 19.1 + - - +
1055B GLN* 3.7 33.6 + - - +
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Residues in contact with THR1107 (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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1088A PHE* 5.4 3.6 - - + -
1091A MET* 3.9 17.9 - - + +
1092A ILE* 3.2 23.7 - - + +
1103A ARG 2.9 17.8 + - - -
1104A LEU* 3.7 5.4 - - - -
1106A ASN* 1.3 75.5 + - - +
1108A LEU* 1.4 61.7 + - - +
1110A GLU* 3.3 19.2 + - - +
1111A GLY 3.5 0.3 + - - -
1112A LYS* 3.2 52.7 + - + +
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Residues in contact with LEU1108 (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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1048A TYR 4.3 3.8 - - - +
1050A PRO* 4.2 20.9 - - + -
1053A LEU* 4.1 24.2 - - + -
1065A TRP* 3.9 32.3 - - + -
1088A PHE* 4.0 25.8 - - + -
1104A LEU* 3.0 31.6 + - + +
1105A VAL* 3.7 5.8 - - - +
1107A THR* 1.4 71.3 - - - +
1109A LYS* 1.4 65.9 + - - +
1111A GLY* 3.1 5.7 + - - -
1112A LYS 3.6 16.4 - - - +
1113A ARG* 2.9 27.8 + - - +
1134A PHE* 3.8 9.1 - - + -
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Residues in contact with LYS1109 (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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1054A MET* 4.0 22.0 - - - -
1105A VAL* 2.9 31.0 + - + +
1106A ASN* 3.4 15.9 + - - +
1108A LEU* 1.4 74.5 - - - +
1110A GLU* 1.3 58.9 + - + +
1111A GLY* 3.1 4.6 + - - -
1134A PHE* 3.7 27.3 - - + -
1054B MET* 4.9 12.7 - - - +
1109B LYS* 3.5 25.6 - - - +
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Residues in contact with GLU1110 (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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1106A ASN* 3.1 38.1 + - - +
1107A THR* 3.5 15.1 + - - +
1108A LEU 3.2 0.6 - - - -
1109A LYS* 1.3 74.3 - - + +
1111A GLY* 1.3 58.1 + - - +
1112A LYS* 3.4 30.7 + - - +
1055B GLN* 5.5 3.3 + - - -
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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