Contacts of the helix formed by residues 1180 - 1187 (chain K) in PDB entry 3F5P
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 SER1180 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1178K TRP 3.9 0.4 + - - -
1179K MET* 1.3 75.4 - - - +
1181K PRO* 1.3 74.2 - - - +
1182K GLU* 3.2 22.1 + - - -
1183K SER* 2.6 31.4 + - - -
1184K LEU* 2.9 22.2 + - - +
1193K SER* 3.2 14.5 + - - -
1196K TRP* 3.7 27.5 - - - -
1256K ARG* 4.0 0.9 - - - -
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Residues in contact with PRO1181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179K MET 3.9 0.2 - - - -
1180K SER* 1.3 87.8 - - - +
1182K GLU* 1.3 62.3 + - - +
1184K LEU* 3.4 6.8 + - + +
1185K LYS* 3.0 32.2 + - - +
1196K TRP* 3.6 30.3 - - + -
1225K VAL* 3.6 30.7 - - + +
1226K MET* 4.3 7.3 - - - +
1251K TYR* 3.5 40.4 - - + +
1256K ARG* 4.0 2.9 - - - +
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Residues in contact with GLU1182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180K SER* 3.2 17.1 + - - +
1181K PRO* 1.3 74.5 - - - +
1183K SER* 1.3 62.4 + - - +
1185K LYS* 4.5 5.2 - - - -
1186K ASP* 3.1 26.7 + - - +
1187K GLY 3.7 2.4 + - - -
1188K VAL* 4.0 22.6 + - + +
1190K THR* 4.8 3.0 + - - +
1192K TYR* 4.5 0.3 - - - +
1193K SER* 3.8 10.7 + - - -
1251K TYR 4.2 2.6 - - - +
1253K PRO* 3.4 28.3 - - + +
1256K ARG* 2.7 41.1 + - - -
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Residues in contact with SER1183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179K MET* 3.6 23.3 - - - +
1180K SER* 2.6 32.0 + - - -
1182K GLU* 1.3 77.3 - - - +
1184K LEU* 1.3 61.0 + - - +
1187K GLY* 2.8 29.0 + - - -
1188K VAL 2.9 23.8 + - - +
1189K PHE* 3.5 14.4 - - - -
1193K SER* 3.5 9.9 - - - -
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Residues in contact with LEU1184 (chain K).
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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1176K VAL* 4.0 29.4 - - + +
1179K MET* 3.8 33.2 - - + +
1180K SER 2.9 21.1 + - - +
1181K PRO* 3.7 4.0 - - + +
1183K SER* 1.3 73.3 - - - +
1185K LYS* 1.3 62.0 + - - +
1186K ASP 3.7 0.2 + - - -
1187K GLY 4.7 0.3 + - - -
1221K VAL* 5.0 0.9 - - + +
1222K LEU* 3.8 40.9 - - + +
1225K VAL* 3.9 30.1 - - + -
1226K MET* 3.8 15.5 - - + +
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Residues in contact with LYS1185 (chain K).
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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1181K PRO 3.0 18.1 + - - +
1182K GLU* 4.1 5.2 - - - +
1183K SER 3.2 0.2 - - - -
1184K LEU* 1.3 80.5 - - - +
1186K ASP* 1.3 82.6 + - - +
1226K MET* 3.8 26.9 - - + +
1251K TYR* 4.9 15.7 + - - +
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Residues in contact with ASP1186 (chain K).
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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1167K ARG* 3.5 32.0 + - - +
1168K LYS 4.9 2.1 - - - +
1182K GLU* 3.1 12.0 + - - +
1185K LYS* 1.3 102.2 - - - +
1187K GLY* 1.3 66.3 + - - +
1188K VAL* 3.3 6.1 + - + +
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Residues in contact with GLY1187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1166K PTR 3.5 2.3 - - - +
1167K ARG* 3.4 2.4 - - - -
1168K LYS* 2.9 36.2 + - - -
1179K MET* 5.6 0.4 - - - -
1183K SER 2.8 19.0 + - - -
1184K LEU 4.6 0.8 + - - -
1186K ASP* 1.3 78.7 - - - +
1188K VAL* 1.3 60.3 + - - +
1189K PHE* 3.5 15.2 - - - -
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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