Contacts of the helix formed by residues 1175 - 1179 (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 PRO1175 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1135K ASP* 4.4 1.3 - - - +
1139K ARG* 3.1 34.3 - - - +
1173K LEU 3.4 5.1 - - - +
1174K LEU* 1.3 96.2 - - + +
1176K VAL* 1.3 64.7 + - - +
1177K ARG* 3.4 2.4 + - + +
1178K TRP* 3.6 33.0 + - + +
1179K MET* 3.5 13.4 + - - +
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Residues in contact with VAL1176 (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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1174K LEU 3.5 6.2 + - - +
1175K PRO* 1.3 68.8 - - - +
1177K ARG* 1.3 71.4 + - + +
1178K TRP 3.1 3.4 - - - -
1179K MET* 3.0 28.1 + - - +
1184K LEU* 4.0 25.4 - - + +
1218K ASN* 3.9 44.6 - - + +
1221K VAL* 4.5 13.5 - - + +
1222K LEU* 4.5 15.5 - - + -
1225K VAL* 5.9 1.0 - - - +
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Residues in contact with ARG1177 (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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1175K PRO* 3.3 2.6 - - + -
1176K VAL* 1.3 83.5 - - + +
1178K TRP* 1.3 80.6 + - + +
1179K MET 3.4 1.3 + - - +
1196K TRP* 4.9 1.6 + - - -
1200K VAL* 4.0 10.7 - - - +
1211K GLN* 3.5 40.0 + - - +
1212K PRO* 2.6 49.4 + - + +
1213K TYR* 3.4 47.8 + - + +
1214K GLN* 3.9 0.4 - - - +
1216K LEU 2.7 24.0 + - - -
1217K SER* 4.1 1.2 - - - +
1218K ASN* 3.4 29.8 + - - +
1221K VAL* 4.0 12.2 - - + +
1225K VAL* 5.8 0.3 - - - +
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Residues in contact with TRP1178 (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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1088K LYS* 4.6 14.6 - - - -
1134K ARG 5.6 1.5 - - - +
1135K ASP* 6.1 1.6 - - - -
1136K LEU 3.4 25.6 - - - +
1137K ALA* 3.5 13.3 - - + +
1139K ARG* 4.0 14.4 - - - +
1175K PRO* 3.6 30.0 + - + +
1176K VAL 3.1 0.8 - - - -
1177K ARG* 1.3 101.3 - - + +
1179K MET* 1.3 62.7 + - - +
1196K TRP* 3.6 9.6 - - - -
1197K SER* 2.9 30.2 + - - +
1200K VAL* 3.3 31.3 - - + +
1201K VAL* 4.8 0.2 - - + -
1204K GLU* 3.0 41.9 + - - -
1211K GLN* 5.9 1.3 - - + -
1212K PRO* 4.0 19.5 - - + -
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Residues in contact with MET1179 (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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1134K ARG 5.6 2.7 - - - +
1174K LEU* 4.1 28.0 - - + +
1175K PRO 3.5 17.7 - - - +
1176K VAL* 3.0 18.1 + - - +
1177K ARG 3.4 1.1 - - - +
1178K TRP* 1.3 79.1 - - + +
1180K SER* 1.3 63.3 + - - +
1181K PRO 3.9 0.5 - - - -
1183K SER* 3.6 38.8 - - - +
1184K LEU* 3.7 32.5 - - + +
1187K GLY* 5.6 0.7 - - - -
1189K PHE* 3.9 19.5 - - + -
1196K TRP* 3.3 12.7 + - - -
1225K VAL* 4.2 5.2 - - - +
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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