Contacts of the helix formed by residues 1180 - 1187 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1178L TRP 3.9 0.4 + - - -
1179L MET* 1.3 77.0 - - - +
1181L PRO* 1.3 76.4 - - - +
1182L GLU* 3.1 27.8 + - - -
1183L SER* 2.8 29.2 + - - -
1184L LEU* 3.0 21.1 + - - +
1193L SER* 3.5 9.1 + - - -
1196L TRP* 3.6 27.7 - - - -
1225L VAL* 4.4 0.2 - - - -
1256L ARG* 4.1 0.9 - - - -
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Residues in contact with PRO1181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180L SER* 1.3 88.1 - - - +
1182L GLU* 1.3 62.1 + - + +
1184L LEU* 3.1 5.6 + - + +
1185L LYS* 3.0 28.7 + - - +
1196L TRP* 3.5 38.1 - - + -
1225L VAL* 3.7 25.1 - - + +
1226L MET* 3.8 9.3 - - + +
1251L TYR* 3.7 40.2 - - + +
1256L ARG* 4.0 4.7 - - - +
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Residues in contact with GLU1182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180L SER* 3.1 17.7 + - - +
1181L PRO* 1.3 75.0 - - - +
1183L SER* 1.3 64.4 + - - +
1185L LYS* 3.9 7.7 - - - +
1186L ASP* 3.5 20.5 + - - +
1188L VAL* 3.9 24.8 + - + +
1190L THR* 4.3 6.8 + - + +
1193L SER* 3.9 10.9 + - - -
1251L TYR* 4.4 2.6 - - + +
1253L PRO* 3.4 27.5 - - + +
1256L ARG* 2.9 40.7 + - - -
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Residues in contact with SER1183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179L MET* 3.7 21.4 - - - +
1180L SER* 2.8 34.5 + - - -
1182L GLU* 1.3 77.2 - - - +
1184L LEU* 1.3 59.3 + - - +
1185L LYS 3.2 0.2 - - - -
1187L GLY* 2.8 27.2 + - - -
1188L VAL 3.0 22.5 + - - +
1189L PHE* 3.7 16.5 - - - -
1193L SER* 3.6 11.1 - - - -
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Residues in contact with LEU1184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176L VAL* 4.3 21.5 - - + +
1179L MET* 3.6 38.6 - - + +
1180L SER 3.0 17.1 + - - +
1181L PRO 3.1 7.2 + - - +
1183L SER* 1.3 77.5 - - - +
1185L LYS* 1.3 61.1 + - - +
1187L GLY 4.9 0.3 + - - -
1221L VAL* 4.8 1.1 - - + +
1222L LEU* 3.5 47.0 - - + +
1225L VAL* 3.9 26.5 - - + -
1226L MET* 3.9 11.2 - - + +
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Residues in contact with LYS1185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181L PRO 3.0 14.4 + - - +
1182L GLU* 3.8 6.0 + - - +
1184L LEU* 1.3 80.3 - - - +
1186L ASP* 1.3 78.7 + - - +
1226L MET* 3.9 27.4 - - + -
1251L TYR* 5.0 12.6 + - - +
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Residues in contact with ASP1186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167L ARG* 3.8 24.7 + - - +
1168L LYS 4.7 3.3 - - - +
1182L GLU* 3.5 8.5 + - - +
1185L LYS* 1.3 114.2 - - - +
1187L GLY* 1.3 64.6 + - - +
1188L VAL* 3.6 18.8 + - + -
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Residues in contact with GLY1187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167L ARG* 3.2 3.9 - - - -
1168L LYS* 2.9 35.7 + - - -
1179L MET* 5.7 0.4 - - - -
1183L SER 2.8 18.7 + - - -
1184L LEU 4.7 0.2 - - - -
1186L ASP* 1.3 78.6 - - - +
1188L VAL* 1.3 60.6 + - - +
1189L PHE* 3.4 17.7 - - - -
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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