Contacts of the helix formed by residues 1223 - 1230 (chain B) in PDB entry 5J67
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 SER1223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1111B ASP* 4.0 17.5 + - - -
1221B ARG 3.8 2.6 + - - -
1222B VAL* 1.3 80.1 - - - +
1224B SER* 1.3 51.8 + - - +
1225B HIS* 3.5 13.3 + - - +
1226B CYS* 3.1 30.6 + - - +
1227B SER* 2.8 33.6 + - - -
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Residues in contact with SER1224 (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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1223B SER* 1.3 73.1 - - - +
1225B HIS* 1.3 71.3 + - - +
1227B SER* 2.9 17.3 + - - -
1228B SER* 3.2 14.2 + - - -
1231B ARG* 5.2 0.5 + - - -
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Residues in contact with HIS1225 (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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793B ARG* 6.1 0.2 - - - +
1111B ASP* 5.9 0.8 + - - -
1136B ARG* 3.7 43.7 + - - -
1139B CYS* 5.7 0.2 - - - -
1223B SER* 3.4 12.0 + - - +
1224B SER* 1.3 82.2 + - - +
1226B CYS* 1.3 65.8 + - - +
1228B SER* 3.4 6.8 + - - -
1229B LEU* 3.2 34.5 + - + +
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Residues in contact with CYS1226 (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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1111B ASP* 3.9 17.9 - - - +
1139B CYS* 2.1 56.3 - - - -
1140B PRO* 4.3 4.9 - - + -
1180B SER* 5.4 0.4 - - - +
1222B VAL* 3.8 15.0 - - + -
1223B SER* 3.1 17.5 + - - +
1225B HIS* 1.3 80.1 - - - +
1227B SER* 1.3 55.2 + - - +
1229B LEU* 3.2 1.7 + - - +
1230B LEU* 2.7 47.4 + - + +
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Residues in contact with SER1227 (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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1183B PHE* 3.2 49.2 - - - -
1222B VAL* 3.7 9.5 - - - +
1223B SER 2.8 24.6 + - - -
1224B SER* 2.9 17.3 + - - -
1226B CYS* 1.3 75.1 - - - +
1228B SER* 1.3 62.6 + - - +
1231B ARG* 3.3 22.9 + - - -
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Residues in contact with SER1228 (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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1224B SER 3.2 10.4 + - - -
1225B HIS* 3.5 10.3 - - - -
1226B CYS 3.2 0.4 - - - -
1227B SER* 1.3 82.1 + - - +
1229B LEU* 1.3 63.2 + - - +
1231B ARG* 3.2 30.9 + - - +
1232B SER* 4.0 2.9 + - - -
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Residues in contact with LEU1229 (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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795B ASP* 3.6 13.9 - - - +
796B GLU* 3.7 29.4 - - + +
797B ALA* 3.5 34.1 - - + +
1139B CYS* 3.8 13.0 - - - -
1225B HIS* 3.2 22.0 + - + +
1226B CYS* 3.7 4.5 - - - +
1228B SER* 1.3 79.4 - - - +
1230B LEU* 1.3 58.7 + - + +
1232B SER* 2.5 31.4 + - - +
1235B ILE* 3.7 0.3 - - - +
1282B TYR* 3.2 35.5 - - + +
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Residues in contact with LEU1230 (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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1139B CYS* 5.3 4.5 - - + -
1140B PRO 5.3 1.1 - - - +
1142B VAL* 3.7 31.4 - - + -
1180B SER* 3.9 30.1 - - - +
1183B PHE* 3.5 26.2 - - + -
1184B ARG* 2.7 31.5 + - - -
1187B HIS* 4.0 5.5 - - - +
1222B VAL* 4.1 13.2 - - + -
1226B CYS* 2.7 36.9 + - + +
1227B SER 3.8 1.3 - - - -
1228B SER 3.2 0.2 - - - -
1229B LEU* 1.3 73.7 - - + +
1231B ARG* 1.3 53.0 + - - +
1232B SER 3.4 0.9 - - - -
1235B ILE* 3.7 18.6 - - + -
1280B ASN* 4.6 7.6 - - - +
1282B TYR* 5.0 2.2 - - + +
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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