Contacts of the helix formed by residues 1099 - 1110 (chain B) in PDB entry 4EI4
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1040A ASP* 3.2 52.3 - - + +
1041A ARG 4.8 2.7 - - - +
1043A SER* 4.5 6.5 - - - +
1045A VAL* 3.7 28.7 - - + -
1048A TYR* 6.2 0.9 - - + -
1052A CYS 4.8 4.5 - - - +
1053A LEU* 3.8 20.4 - - + +
1056A SER* 5.3 2.7 - - - +
1101A VAL* 4.0 16.6 - - + -
1096B HIS* 2.8 14.7 + - + +
1098B GLN* 1.3 80.9 - - - +
1100B THR* 1.3 64.3 + - - +
1101B VAL 3.4 2.2 - - - -
1102B THR* 2.9 42.1 - - + +
1103B ARG* 3.0 10.6 + - - +
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Residues in contact with THR1100 (chain B).
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* 5.1 11.0 - - - +
1045B VAL* 5.8 0.2 - - + -
1046B PHE* 3.8 23.8 - - + -
1089B LEU* 4.2 10.1 - - + +
1092B ILE* 3.8 20.5 - - + +
1093B GLY 5.4 0.7 - - - +
1094B PRO 5.8 1.4 + - - -
1096B HIS* 3.9 11.6 + - - +
1097B GLY* 2.9 30.2 + - - -
1098B GLN 3.4 1.0 - - - -
1099B MET* 1.3 77.6 - - - +
1101B VAL* 1.3 56.8 + - + +
1103B ARG* 3.2 6.4 + - - +
1104B LEU* 2.8 32.4 + - - +
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Residues in contact with VAL1101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098A GLN* 3.9 35.6 + - + +
1099A MET* 4.0 16.6 - - + -
1102A THR* 3.3 23.3 - - - +
1045B VAL* 3.6 34.1 - - + -
1053B LEU* 4.2 14.8 - - + -
1098B GLN 4.8 1.6 + - - +
1099B MET 3.4 0.4 - - - -
1100B THR* 1.3 80.1 - - + +
1102B THR* 1.3 57.6 + - - +
1104B LEU* 3.3 7.9 + - + +
1105B VAL* 2.9 35.6 + - + +
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Residues in contact with THR1102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053A LEU 3.0 19.0 + - - +
1054A MET* 3.7 13.3 + - - +
1101A VAL* 4.3 15.0 - - + +
1102A THR* 4.6 7.6 + - - -
1105A VAL* 5.3 3.8 - - - +
1098B GLN 5.0 0.8 + - - +
1099B MET* 2.9 55.9 - - + +
1101B VAL* 1.3 80.9 - - - +
1103B ARG* 1.3 58.4 + - + +
1105B VAL* 3.5 7.9 + - - +
1106B ASN* 3.0 27.7 + - - +
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Residues in contact with ARG1103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037A VAL 3.1 21.4 + - - -
1038A LYS* 3.1 25.5 + - - +
1040A ASP* 2.9 25.6 + - - +
1054A MET 5.9 0.2 - - - -
1056A SER* 3.7 14.3 + - - +
1092B ILE* 4.0 17.9 + - + +
1096B HIS* 3.2 38.9 + - - -
1099B MET 3.0 14.6 + - - +
1100B THR* 3.6 8.1 - - - +
1102B THR* 1.3 77.5 - - + +
1104B LEU* 1.3 59.0 + - - +
1106B ASN* 3.4 7.5 + - - +
1107B THR* 2.9 32.0 + - - -
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Residues in contact with LEU1104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B VAL* 3.5 33.9 - - + +
1046B PHE* 3.9 20.9 - - + -
1053B LEU* 3.7 20.2 - - + -
1088B PHE* 3.7 42.6 - - + -
1092B ILE* 4.1 12.7 - - + +
1100B THR* 2.8 17.2 + - + +
1101B VAL* 3.4 10.5 - - - +
1103B ARG* 1.3 70.9 - - - +
1105B VAL* 1.3 65.3 + - - +
1107B THR* 3.2 8.9 + - - -
1108B LEU* 2.9 34.8 + - + +
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Residues in contact with VAL1105 (chain B).
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* 5.1 3.8 - - + -
1050B PRO* 5.5 3.4 - - + -
1053B LEU* 3.7 34.8 - - + +
1054B MET* 3.6 35.7 - - + -
1101B VAL* 2.9 28.9 + - + +
1102B THR* 3.7 7.9 - - - +
1104B LEU* 1.3 72.8 - - - +
1106B ASN* 1.3 57.7 + - - +
1108B LEU* 3.4 10.1 + - - +
1109B LYS* 2.9 38.6 + - + +
1134B PHE* 4.9 0.3 - - - -
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Residues in contact with ASN1106 (chain B).
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* 3.6 20.8 + - - +
1055A GLN* 4.1 25.5 + - - +
1102B THR 3.0 17.7 + - - +
1103B ARG* 3.5 9.4 - - + +
1105B VAL* 1.3 75.3 - - - +
1107B THR* 1.3 65.1 + - - +
1109B LYS* 3.2 16.4 + - - +
1110B GLU* 3.1 46.4 + - - +
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Residues in contact with THR1107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088B PHE* 4.9 8.1 - - + -
1091B MET* 4.8 13.3 + - + -
1092B ILE* 2.9 34.1 - - + +
1103B ARG 2.9 12.0 + - - -
1104B LEU* 3.4 9.0 - - - -
1106B ASN* 1.3 76.2 - - - +
1108B LEU* 1.3 60.4 + - - +
1110B GLU* 3.3 19.3 + - - +
1111B GLY 3.4 0.3 + - - -
1112B LYS* 3.3 52.9 + - + +
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Residues in contact with LEU1108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048B TYR 4.5 2.5 - - - +
1050B PRO* 4.1 18.4 - - + -
1053B LEU* 4.0 25.8 - - + -
1065B TRP* 3.7 29.6 - - + -
1088B PHE* 4.4 21.1 - - + -
1104B LEU* 2.9 29.5 + - + +
1105B VAL* 3.8 6.5 - - - +
1107B THR* 1.3 72.5 - - - +
1109B LYS* 1.3 65.7 + - - +
1111B GLY* 3.2 4.2 + - - -
1112B LYS 3.9 13.7 - - - +
1113B ARG* 3.1 32.0 + - - +
1134B PHE* 3.7 14.5 - - + -
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Residues in contact with LYS1109 (chain B).
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* 5.5 6.5 - - - -
1109A LYS* 4.3 18.2 - - - +
1054B MET* 4.0 22.8 - - - -
1105B VAL* 2.9 28.3 + - + +
1106B ASN* 3.5 18.2 - - - +
1108B LEU* 1.3 79.0 - - - +
1110B GLU* 1.3 63.3 + - + +
1111B GLY* 3.2 1.9 + - - -
1134B PHE* 3.8 24.9 - - + -
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Residues in contact with GLU1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106B ASN* 3.1 34.5 + - - +
1107B THR* 3.6 12.3 + - - +
1108B LEU 3.3 0.4 - - - -
1109B LYS* 1.3 74.8 - - + +
1111B GLY* 1.3 58.1 + - - +
1112B LYS* 3.5 27.9 + - + +
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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