Contacts of the helix formed by residues 1258 - 1265 (chain G) 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 SER1258 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195G VAL* 4.7 2.5 - - - -
1257G PRO* 1.3 75.0 - - - +
1259G PHE* 1.3 65.0 + - - +
1260G LEU* 3.5 9.6 + - - +
1261G GLU* 2.9 40.7 + - - +
1262G ILE* 3.0 25.2 + - - +
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Residues in contact with PHE1259 (chain G).
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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1120G ALA* 3.6 13.4 - - - +
1123G MET* 3.6 53.8 - - + -
1124G ALA* 3.6 20.4 - - + -
1127G ASN* 3.5 27.1 - - + -
1194G ASP* 3.7 8.7 - - + -
1195G VAL* 3.7 31.8 - - + +
1198G PHE* 3.6 30.1 - + + -
1257G PRO 4.3 0.2 + - - -
1258G SER* 1.3 73.2 - - - +
1260G LEU* 1.3 58.4 + - - +
1262G ILE* 3.2 15.3 + - + +
1263G ILE* 2.9 34.9 + - - +
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Residues in contact with LEU1260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124G ALA* 4.0 21.5 - - + +
1258G SER* 3.1 9.3 + - - +
1259G PHE* 1.3 78.5 - - - +
1261G GLU* 1.3 56.8 + - + +
1263G ILE* 3.3 4.9 + - + +
1264G SER* 2.8 29.5 + - - -
1279G PHE* 4.2 9.0 - - + -
1280G TYR* 3.7 22.8 - - + -
1285G ASN* 3.6 39.9 - - - +
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Residues in contact with GLU1261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256G ARG 4.3 2.3 - - - +
1257G PRO* 3.4 9.0 - - - +
1258G SER* 2.9 46.8 + - - +
1260G LEU* 1.3 72.1 - - + +
1262G ILE* 1.3 66.7 + - - +
1264G SER* 3.2 8.5 + - - -
1265G SER* 3.1 22.7 + - - -
986H VAL* 4.0 31.4 - - + +
987H TYR* 4.3 21.7 - - - +
989H PRO* 6.0 0.7 - - - +
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Residues in contact with ILE1262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120G ALA* 4.2 10.5 - - + -
1195G VAL* 4.4 5.6 - - + -
1198G PHE* 3.7 42.4 - - + -
1244G LEU* 4.3 23.3 - - + -
1248G CYS* 4.1 12.1 - - - -
1257G PRO* 3.7 18.4 - - + +
1258G SER 3.0 21.4 + - - +
1259G PHE* 3.3 21.8 - - + +
1261G GLU* 1.3 75.2 - - - +
1263G ILE* 1.3 64.1 + - - +
1265G SER* 2.6 25.2 + - - -
1266G ILE* 3.6 14.4 + - + +
986H VAL* 5.0 2.2 - - - -
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Residues in contact with ILE1263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117G GLY* 4.2 5.4 - - - +
1120G ALA* 3.4 23.6 - - + +
1121G ASP* 3.3 42.4 - - - +
1124G ALA* 4.1 9.6 - - + -
1259G PHE 2.9 21.1 + - - +
1260G LEU* 3.8 6.7 - - - +
1262G ILE* 1.3 73.0 - - - +
1264G SER* 1.3 66.9 + - - +
1265G SER 3.1 0.2 + - - -
1266G ILE* 3.2 10.2 + - + +
1267G LYS* 2.9 25.7 + - + +
1270G MET* 5.7 0.7 - - + -
1274G PHE* 4.0 23.1 - - + -
1280G TYR* 3.8 27.4 - - + -
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Residues in contact with SER1264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260G LEU 2.8 17.9 + - - -
1261G GLU* 3.2 9.4 + - - -
1263G ILE* 1.3 76.8 - - - +
1265G SER* 1.3 60.9 + - - +
1267G LYS* 3.2 34.9 + - - +
1268G GLU 5.0 0.2 + - - -
1280G TYR* 3.5 22.3 + - - -
986H VAL 5.7 1.0 + - - -
989H PRO* 5.9 0.5 - - - +
990H ASP* 4.4 13.9 + - - +
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Residues in contact with SER1265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244G LEU* 5.5 2.4 - - - +
1261G GLU 3.1 10.8 + - - -
1262G ILE* 2.6 25.3 + - - +
1264G SER* 1.3 77.1 - - - +
1266G ILE* 1.3 65.2 + - - +
1269G GLU* 5.0 3.1 - - - +
981H PHE* 3.9 23.9 - - - -
985H ASP* 3.9 10.3 - - - +
986H VAL* 3.8 30.1 - - - +
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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