Contacts of the helix formed by residues 1258 - 1265 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195D VAL* 4.6 3.1 - - - -
1256D ARG 3.8 0.6 + - - -
1257D PRO* 1.3 73.6 - - - +
1259D PHE* 1.3 59.4 + - - +
1260D LEU* 3.2 10.2 + - - +
1261D GLU* 2.8 46.6 + - - +
1262D ILE* 3.0 31.9 + - - +
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Residues in contact with PHE1259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120D ALA* 3.5 26.9 - - + +
1123D MET* 3.4 50.5 - - + -
1124D ALA* 3.8 10.5 - - + -
1127D ASN* 3.2 29.2 - - + -
1194D ASP* 3.6 26.2 - - + -
1195D VAL* 3.7 14.3 - - + +
1198D PHE* 3.5 33.2 - + + -
1258D SER* 1.3 73.6 - - - +
1260D LEU* 1.3 62.2 + - - +
1262D ILE* 3.8 10.6 - - + +
1263D ILE* 3.2 30.7 + - - +
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Residues in contact with LEU1260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124D ALA* 3.7 25.8 - - + +
1258D SER* 3.1 8.6 + - - +
1259D PHE* 1.3 77.6 - - - +
1261D GLU* 1.3 65.9 + - + +
1263D ILE* 3.3 6.0 + - + +
1264D SER* 2.9 23.7 + - - -
1279D PHE* 4.2 9.9 - - + -
1280D TYR* 3.7 29.4 - - + -
1285D ASN* 3.6 28.3 - - - +
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Residues in contact with GLU1261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256D ARG 4.6 1.6 - - - +
1257D PRO* 3.6 7.4 - - + +
1258D SER* 2.8 40.6 + - - +
1260D LEU* 1.3 77.6 - - + +
1262D ILE* 1.3 62.9 + - - +
1264D SER* 3.1 16.7 + - - -
1265D SER* 3.3 13.2 + - - -
986G VAL* 3.7 29.8 - - + +
987G TYR* 4.4 22.4 - - - +
989G PRO* 6.0 1.0 - - - +
1049G ASN* 5.6 2.8 + - - -
1052G SER* 5.8 0.2 + - - -
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Residues in contact with ILE1262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116D ALA* 6.0 0.2 - - + -
1120D ALA* 4.4 6.3 - - + -
1195D VAL* 4.4 7.9 - - + -
1198D PHE* 3.7 39.5 - - + -
1244D LEU* 4.0 28.9 - - + -
1248D CYS* 3.8 18.4 - - - -
1257D PRO* 3.6 17.9 - - + -
1258D SER 3.0 17.9 + - - +
1259D PHE* 3.8 13.5 - - + +
1260D LEU 3.3 0.2 - - - -
1261D GLU* 1.3 74.2 - - - +
1263D ILE* 1.3 63.5 + - - +
1265D SER* 2.6 25.1 + - - -
1266D ILE* 3.6 14.4 + - + +
986G VAL* 4.5 4.0 - - + +
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Residues in contact with ILE1263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117D GLY* 4.2 10.1 - - - +
1120D ALA* 3.4 19.5 - - + +
1121D ASP* 3.4 38.8 - - + +
1124D ALA* 4.0 9.0 - - + -
1259D PHE 3.2 20.0 + - - +
1260D LEU* 3.3 4.5 + - + +
1262D ILE* 1.3 78.2 - - - +
1264D SER* 1.3 58.4 + - - +
1265D SER 3.0 0.5 + - - -
1266D ILE* 3.0 9.7 + - + +
1267D LYS* 2.8 30.6 + - + +
1270D MET* 6.1 0.4 - - + -
1274D PHE* 4.2 14.8 - - + -
1280D TYR* 3.4 39.5 - - + -
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Residues in contact with SER1264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260D LEU 2.9 13.2 + - - -
1261D GLU* 3.1 13.6 + - - -
1263D ILE* 1.3 76.4 - - - +
1265D SER* 1.3 57.9 + - - +
1266D ILE 3.4 0.2 - - - -
1267D LYS* 3.3 33.1 + - - +
1280D TYR* 3.3 25.8 + - - -
986G VAL 5.9 0.4 - - - -
989G PRO* 5.7 1.9 - - - +
990G ASP* 3.8 19.1 + - - +
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Residues in contact with SER1265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244D LEU* 5.3 2.3 - - - +
1261D GLU 3.3 7.8 + - - -
1262D ILE* 2.6 24.6 + - - +
1263D ILE 3.0 0.2 + - - -
1264D SER* 1.3 79.0 - - - +
1266D ILE* 1.3 65.3 + - - +
1267D LYS 3.7 0.2 - - - -
1268D GLU* 6.4 0.7 - - - -
1269D GLU* 5.1 2.4 - - - +
981G PHE* 4.1 23.9 - - - -
985G ASP 3.9 15.3 - - - -
986G VAL* 3.9 22.3 - - - +
990G ASP* 5.2 2.5 - - - -
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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