Contacts of the helix formed by residues 1258 - 1265 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195T VAL* 4.7 2.2 - - - -
1256T ARG 3.8 1.0 + - - -
1257T PRO* 1.3 73.2 - - - +
1259T PHE* 1.3 59.3 + - - +
1260T LEU* 3.1 13.1 + - - +
1261T GLU* 2.8 41.2 + - - +
1262T ILE* 3.0 31.9 + - - +
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Residues in contact with PHE1259 (chain T).
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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1120T ALA* 3.6 25.7 - - + +
1123T MET* 3.5 51.6 - - + -
1124T ALA* 3.8 11.9 - - + -
1127T ASN* 3.1 28.3 - - - -
1191T THR 4.6 0.2 - - - -
1194T ASP* 3.8 16.8 - - + -
1195T VAL* 3.7 26.0 - - + +
1198T PHE* 3.6 31.4 - + + -
1258T SER* 1.3 74.0 - - - +
1260T LEU* 1.3 57.7 + - - +
1262T ILE* 3.4 8.1 + - + +
1263T ILE* 2.9 36.5 + - - +
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Residues in contact with LEU1260 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124T ALA* 4.2 21.8 - - + +
1258T SER* 3.1 9.3 + - - +
1259T PHE* 1.3 75.9 - - + +
1261T GLU* 1.3 60.3 + - + +
1263T ILE* 3.3 5.6 + - - +
1264T SER* 2.9 30.9 + - - -
1279T PHE* 4.3 6.3 - - + -
1280T TYR* 3.7 19.0 - - + -
1285T ASN* 3.5 38.4 - - - +
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Residues in contact with GLU1261 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986I VAL* 3.4 31.1 - - + +
987I TYR* 4.2 21.5 - - - +
1049I ASN* 5.8 1.0 + - - -
1256T ARG 4.4 1.9 - - - +
1257T PRO* 3.3 9.9 - - + +
1258T SER* 2.8 45.4 + - - +
1260T LEU* 1.3 74.7 - - + +
1262T ILE* 1.3 65.0 + - - +
1264T SER* 3.1 8.2 + - - -
1265T SER* 3.0 24.6 + - - -
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Residues in contact with ILE1262 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986I VAL* 4.8 3.4 - - + -
1120T ALA* 4.4 7.0 - - + -
1195T VAL* 4.5 6.5 - - + -
1198T PHE* 3.8 31.2 - - + -
1244T LEU* 4.2 24.7 - - + -
1248T CYS* 3.7 30.1 - - - -
1257T PRO* 3.7 20.9 - - + -
1258T SER 3.0 20.7 + - - +
1259T PHE* 3.7 12.8 - - + +
1260T LEU 3.3 0.2 - - - -
1261T GLU* 1.3 74.3 - - - +
1263T ILE* 1.3 65.4 + - - +
1265T SER* 3.2 21.0 + - - -
1266T ILE* 3.6 13.7 + - + +
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Residues in contact with ILE1263 (chain T).
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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1117T GLY* 4.3 4.0 - - - +
1120T ALA* 3.7 19.3 - - + +
1121T ASP* 3.3 42.4 - - + +
1124T ALA* 4.2 9.4 - - + -
1259T PHE 2.9 21.8 + - - +
1260T LEU* 3.6 4.5 - - - +
1262T ILE* 1.3 77.7 - - - +
1264T SER* 1.3 53.5 + - - +
1266T ILE* 3.0 10.9 + - + +
1267T LYS* 2.8 35.8 + - + -
1270T MET* 5.9 0.7 - - + -
1274T PHE* 4.0 17.5 - - + -
1280T TYR* 3.6 35.2 - - + -
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Residues in contact with SER1264 (chain T).
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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985I ASP 5.1 0.2 - - - -
986I VAL* 5.5 2.5 - - - -
988I VAL 5.9 1.8 - - - -
989I PRO* 5.9 2.7 - - - +
990I ASP* 3.5 18.5 + - - +
1260T LEU 2.9 12.9 + - - -
1261T GLU* 3.1 11.9 + - - -
1263T ILE* 1.3 76.3 - - - +
1265T SER* 1.3 61.0 + - - +
1266T ILE 3.2 1.0 + - - -
1267T LYS* 3.2 30.8 + - - +
1268T GLU 5.1 0.2 + - - -
1280T TYR* 2.4 34.6 + - - -
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Residues in contact with SER1265 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981I PHE* 3.1 30.6 - - - -
985I ASP* 3.5 26.5 + - - +
986I VAL* 3.5 25.6 - - - +
990I ASP* 5.1 0.7 - - - -
1244T LEU* 5.1 1.6 - - - +
1261T GLU 3.0 6.9 + - - -
1262T ILE* 3.2 11.4 + - - -
1263T ILE 3.2 0.6 - - - -
1264T SER* 1.3 75.5 - - - +
1266T ILE* 1.3 64.7 + - - +
1269T GLU* 5.6 0.3 - - - +
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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