Contacts of the helix formed by residues 1200 - 1208 (chain B) in PDB entry 4Z4Q
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 LYS1200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198B THR 3.5 3.7 + - - +
1199B ALA* 1.3 75.5 - - - +
1201B ILE* 1.3 68.5 + - - +
1202B ASP* 3.4 7.0 - - + +
1203B LYS* 3.3 17.7 + - + +
1204B LEU* 3.3 13.7 + - - +
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Residues in contact with ILE1201 (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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1200B LYS* 1.3 75.0 - - - +
1202B ASP* 1.3 74.4 + - - +
1203B LYS 3.1 0.2 + - - -
1204B LEU* 3.2 7.3 + - - +
1205B MET* 2.9 47.9 + - + +
1226B LYS* 4.8 9.4 - - + -
1229B TYR* 3.9 25.4 - - + +
1230B GLU* 3.9 32.5 - - + +
1342B ILE* 4.1 10.3 - - + -
1343B VAL* 4.1 24.2 - - + -
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Residues in contact with ASP1202 (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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1200B LYS* 4.6 5.3 - - + +
1201B ILE* 1.3 85.2 - - - +
1203B LYS* 1.3 60.2 + - - +
1205B MET* 3.6 15.3 + - - +
1206B GLU* 3.8 5.7 + - - +
1226B LYS* 5.6 4.3 - - - +
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Residues in contact with LYS1203 (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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1192B TYR* 3.6 35.0 - - + +
1199B ALA* 5.3 0.2 - - + -
1200B LYS* 3.3 15.3 + - + +
1201B ILE 3.1 0.6 - - - -
1202B ASP* 1.3 75.8 - - - +
1204B LEU* 1.3 65.1 + - - +
1205B MET 3.0 1.8 - - - -
1206B GLU* 2.9 24.5 + - + +
1207B PHE* 3.7 9.7 - - + -
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Residues in contact with LEU1204 (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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1189B ALA* 4.4 15.7 - - + +
1192B TYR* 4.4 8.5 - - + -
1193B MET* 4.3 23.6 - - + -
1199B ALA* 4.0 20.6 - - + +
1200B LYS 3.3 16.1 + - - +
1201B ILE* 3.2 9.7 + - - +
1203B LYS* 1.3 75.7 - - - +
1205B MET* 1.3 60.2 + - + +
1207B PHE* 2.9 15.2 + - - +
1208B LEU* 2.7 28.6 + - + +
1342B ILE* 3.5 33.0 - - + -
1343B VAL* 3.7 18.2 - - + -
1346B LEU* 4.7 8.7 - - + -
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Residues in contact with MET1205 (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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1201B ILE* 2.9 37.6 + - + +
1202B ASP* 3.8 10.1 - - - +
1203B LYS 3.0 0.4 - - - -
1204B LEU* 1.3 77.4 - - + +
1206B GLU* 1.3 61.8 + - - +
1207B PHE 3.2 0.2 - - - -
1208B LEU 3.4 14.4 - - - +
1209B PRO* 3.4 43.4 - - + +
1222B ARG* 4.5 18.4 - - + +
1225B ILE* 3.9 17.0 - - + -
1226B LYS* 4.0 18.6 - - + +
1229B TYR* 3.8 18.6 - - + -
1342B ILE* 6.5 0.7 - - + -
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Residues in contact with GLU1206 (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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1202B ASP 3.8 4.6 + - - +
1203B LYS* 2.9 17.9 + - + +
1205B MET* 1.3 77.7 - - - +
1207B PHE* 1.3 69.2 + - + +
1209B PRO* 5.2 2.1 - - - +
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Residues in contact with PHE1207 (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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1185B GLU* 3.3 21.6 - - - +
1188B ASP* 4.1 23.1 - - + +
1189B ALA* 3.7 20.0 - - - +
1192B TYR* 3.2 52.3 - + + -
1203B LYS* 3.7 18.4 - - + -
1204B LEU* 2.9 9.9 + - - +
1206B GLU* 1.3 88.6 - - + +
1208B LEU* 1.3 58.7 + - - +
1209B PRO* 3.3 10.2 - - - +
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Residues in contact with LEU1208 (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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1163B LEU* 4.6 9.0 - - + -
1181B HIS* 3.6 30.3 - - + -
1182B ASN 5.8 0.2 - - - +
1185B GLU* 4.3 9.2 - - + +
1186B VAL* 4.4 18.2 - - + +
1189B ALA* 4.1 17.7 - - + -
1204B LEU* 2.7 16.2 + - + +
1205B MET* 3.4 14.7 - - - +
1207B PHE* 1.3 70.4 - - - +
1209B PRO* 1.3 67.4 - - + +
1210B GLY 3.5 8.8 + - - +
1229B TYR* 3.5 24.0 - - + +
1342B ILE* 3.8 35.0 - - + -
1346B LEU* 5.4 0.9 - - + -
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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