Contacts of the helix formed by residues 1108 - 1123 (chain B) in PDB entry 4EC0
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 LYS1108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106B GLU* 3.0 18.8 + - - +
1107B LYS* 1.3 102.0 - - + +
1109B GLN* 1.3 52.0 + - - +
1110B ASP* 2.7 10.8 + - + -
1111B VAL* 3.0 26.3 + - + -
1112B LYS* 2.7 34.6 + - - -
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Residues in contact with GLN1109 (chain B).
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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1107B LYS 2.9 13.6 + - - -
1108B LYS* 1.3 69.5 - - - +
1110B ASP* 1.3 63.7 + - - +
1112B LYS* 3.9 8.1 - - - +
1113B GLU* 3.0 33.8 + - - +
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Residues in contact with ASP1110 (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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1108B LYS 2.7 5.6 + - - -
1109B GLN* 1.3 78.2 - - - +
1111B VAL* 1.3 59.9 + - + +
1112B LYS 3.0 3.6 - - - -
1113B GLU* 2.8 30.4 + - - +
1114B GLN* 3.0 12.7 + - - +
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Residues in contact with VAL1111 (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 GLU* 3.2 30.1 - - - +
1108B LYS* 3.0 28.9 + - + -
1110B ASP* 1.3 75.7 - - + +
1112B LYS* 1.3 59.4 + - - +
1114B GLN* 3.7 11.6 - - - +
1115B MET* 3.5 18.4 + - - +
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Residues in contact with LYS1112 (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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1103B PRO* 3.8 4.9 - - - -
1104B TRP* 3.4 23.3 + - - +
1105B ALA 4.3 0.6 + - - -
1106B GLU* 2.8 57.7 + - + +
1107B LYS* 4.9 2.0 - - - -
1108B LYS 2.7 17.9 + - - +
1109B GLN* 3.9 9.0 - - - +
1111B VAL* 1.3 69.2 - - - +
1113B GLU* 1.3 59.6 + - - +
1114B GLN 2.9 4.8 + - - -
1115B MET* 3.2 4.2 + - - +
1116B PHE* 2.9 55.1 + - + +
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Residues in contact with GLU1113 (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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1109B GLN* 3.0 22.3 + - - +
1110B ASP* 2.8 9.6 + - - +
1112B LYS* 1.3 80.2 - - - +
1114B GLN* 1.3 56.3 + - - +
1116B PHE* 4.0 9.2 - - + -
1117B ASN* 2.5 52.6 + - - +
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Residues in contact with GLN1114 (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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1110B ASP 3.0 10.5 + - - +
1111B VAL* 3.8 13.5 - - - +
1112B LYS 2.9 0.6 - - - -
1113B GLU* 1.3 83.7 + - - +
1115B MET* 1.3 61.7 + - - +
1116B PHE 3.2 0.9 - - - -
1117B ASN* 3.7 9.4 - - - +
1118B GLU* 3.0 57.9 + - - +
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Residues in contact with MET1115 (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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1101B CYS 5.1 1.8 - - - +
1103B PRO* 3.5 37.0 - - + -
1111B VAL 3.5 10.1 + - - +
1112B LYS 3.2 4.6 + - - +
1114B GLN* 1.3 78.2 - - - +
1116B PHE* 1.3 63.2 + - - +
1118B GLU* 3.3 28.0 - - + +
1119B LEU* 3.2 45.0 + - + +
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Residues in contact with PHE1116 (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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1102B PHE* 3.7 27.6 - + + -
1103B PRO* 3.6 39.9 - - + -
1104B TRP* 3.5 43.1 - + - -
1112B LYS* 2.9 42.7 + - + +
1113B GLU* 4.0 10.1 - - + +
1115B MET* 1.3 76.5 - - - +
1117B ASN* 1.3 58.1 + - - +
1119B LEU* 3.3 2.4 + - - +
1120B LEU* 2.9 43.5 + - + +
1163B PHE* 4.0 29.6 - + - -
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Residues in contact with ASN1117 (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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1113B GLU* 2.5 43.2 + - - +
1114B GLN* 3.8 15.4 - - - +
1115B MET 3.4 0.2 - - - -
1116B PHE* 1.3 79.7 - - - +
1118B GLU* 1.3 56.6 + - + +
1120B LEU* 4.7 7.6 - - - +
1121B THR* 2.7 44.4 + - - +
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Residues in contact with GLU1118 (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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1114B GLN* 3.0 46.7 + - - +
1115B MET* 3.3 30.6 - - + +
1116B PHE 3.3 0.2 - - - -
1117B ASN* 1.3 74.6 - - - +
1119B LEU* 1.3 59.3 + - - +
1122B TYR* 2.8 66.3 + - + +
1123B ASN* 3.4 3.5 - - - +
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Residues in contact with LEU1119 (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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1098B PHE* 3.8 25.8 - - + -
1101B CYS* 3.6 40.4 - - + +
1102B PHE* 3.8 34.1 - - + -
1103B PRO* 4.5 1.3 - - + -
1115B MET* 3.2 34.8 + - + +
1116B PHE 3.7 3.4 - - - +
1118B GLU* 1.3 80.3 - - + +
1120B LEU* 1.3 56.7 + - - +
1123B ASN* 3.0 23.8 + - - +
1124B ALA* 2.8 27.5 + - - +
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Residues in contact with LEU1120 (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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1102B PHE* 3.9 15.0 - - + -
1116B PHE* 2.9 33.6 + - + +
1117B ASN* 4.2 7.6 - - - +
1119B LEU* 1.3 76.1 - - - +
1121B THR* 1.3 60.1 + - - +
1124B ALA* 3.5 7.0 - - + +
1125B PRO* 3.3 13.0 - - - +
1160B LEU* 4.0 34.3 - - + +
1163B PHE* 3.6 29.6 - - + +
1164B LYS* 3.2 51.9 - - + +
1167B LEU* 5.7 0.2 - - + -
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Residues in contact with THR1121 (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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1117B ASN* 2.7 32.6 + - - +
1120B LEU* 1.3 79.9 - - - +
1122B TYR* 1.3 81.6 + - + +
1125B PRO* 3.7 15.3 - - - +
1164B LYS* 4.3 11.2 + - - +
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Residues in contact with TYR1122 (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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1118B GLU* 2.8 50.4 + - + +
1121B THR* 1.3 98.3 - - + +
1123B ASN* 1.3 65.3 + - - +
1125B PRO* 4.3 3.5 - - - +
1126B HIS* 4.8 8.8 + - - +
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Residues in contact with ASN1123 (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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1098B PHE* 3.8 17.2 - - + -
1118B GLU* 3.4 15.1 - - - +
1119B LEU* 3.0 23.3 + - + +
1122B TYR* 1.3 85.3 + - - +
1124B ALA* 1.3 66.9 + - - +
1125B PRO* 3.3 2.7 - - - -
1126B HIS* 3.1 18.0 + - - +
1127B LEU* 3.2 11.1 + - - +
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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