Contacts of the helix formed by residues 1266 - 1270 (chain I) 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 ILE1266 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113I ILE* 4.1 23.1 - - + +
1116I ALA* 4.4 7.6 - - + -
1117I GLY* 3.7 35.2 - - - +
1120I ALA* 5.8 0.2 - - + -
1240I MET* 3.8 28.3 - - + -
1244I LEU* 4.9 4.9 - - + -
1262I ILE* 3.5 15.5 - - + +
1263I ILE* 3.0 17.0 + - + +
1265I SER* 1.3 91.5 - - - +
1267I LYS* 1.3 62.9 + - - +
1268I GLU* 3.1 3.4 - - - -
1269I GLU* 2.8 31.9 + - + +
1270I MET* 3.6 9.8 + - - +
981J PHE* 4.5 0.2 - - + -
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Residues in contact with LYS1267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263I ILE* 2.8 20.7 + - + +
1264I SER* 3.6 23.2 + - - +
1265I SER 3.8 0.4 - - - -
1266I ILE* 1.3 78.2 - - - +
1268I GLU* 1.3 85.6 + - - +
1269I GLU 3.0 4.5 + - - -
1270I MET* 3.3 27.1 + - + +
1274I PHE* 5.2 3.3 - - + -
1280I TYR* 3.7 27.2 + - + +
1281I TYR* 3.4 33.4 + - + +
990J ASP* 4.5 18.0 - - - +
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Residues in contact with GLU1268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276C GLU* 6.1 4.9 - - + -
1266I ILE 3.0 1.2 + - - -
1267I LYS* 1.3 109.6 - - + +
1269I GLU* 1.3 68.0 + - - +
1270I MET 3.5 4.1 + - - +
1275I ARG* 4.8 7.6 + - - -
1281I TYR* 4.3 5.0 + - - -
990J ASP* 6.0 1.2 - - - -
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Residues in contact with GLU1269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109I LEU* 6.4 2.0 - - + -
1110I SER* 4.5 17.9 + - - +
1113I ILE* 3.9 26.8 - - + +
1114I GLN* 4.4 2.6 - - - +
1266I ILE* 2.8 17.1 + - + +
1268I GLU* 1.3 90.2 + - - +
1270I MET* 1.3 60.8 + - - +
1271I GLU 4.2 0.3 + - - -
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Residues in contact with MET1270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113I ILE* 3.9 24.9 - - - +
1114I GLN* 3.3 44.9 - - - +
1117I GLY* 3.9 19.1 - - - -
1118I GLU* 4.0 1.6 - - + +
1263I ILE* 6.0 0.7 - - + -
1266I ILE* 3.7 12.3 - - + +
1267I LYS* 3.3 23.4 + - - +
1268I GLU 4.5 3.3 - - - +
1269I GLU* 1.3 81.6 - - - +
1271I GLU* 1.3 63.4 + - - +
1272I PRO* 3.8 1.9 - - - +
1274I PHE* 3.8 45.8 - - + -
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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