Contacts of the helix formed by residues 1258 - 1267 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195M VAL* 4.6 4.3 - - - -
1256M ARG 3.8 0.8 + - - -
1257M PRO* 1.3 72.6 - - - +
1259M PHE* 1.3 62.1 + - - +
1260M LEU* 3.4 11.1 + - - +
1261M GLU* 2.8 37.8 + - - +
1262M ILE* 2.9 28.7 + - - +
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Residues in contact with PHE1259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120M ALA* 3.7 16.6 - - + +
1123M MET* 3.5 47.6 - - + -
1124M ALA* 3.6 21.5 - - + -
1127M ASN* 3.0 29.6 - - + -
1191M THR* 4.5 0.4 - - - -
1194M ASP* 4.1 4.7 - - + -
1195M VAL* 3.7 35.4 - - + -
1198M PHE* 3.6 33.0 - + + -
1258M SER* 1.3 74.6 - - - +
1260M LEU* 1.3 59.7 + - - +
1262M ILE* 3.4 9.0 + - + +
1263M ILE* 3.1 34.9 + - - +
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Residues in contact with LEU1260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124M ALA* 3.5 25.4 - - + +
1258M SER* 3.2 8.7 - - - +
1259M PHE* 1.3 75.1 - - - +
1261M GLU* 1.3 64.8 + - + +
1263M ILE* 3.3 2.9 + - + -
1264M SER* 2.9 25.1 + - - -
1279M PHE* 4.4 8.1 - - + -
1280M TYR* 3.6 29.3 - - + -
1285M ASN* 3.4 32.1 - - - +
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Residues in contact with GLU1261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986L VAL* 3.4 34.3 - - + +
987L TYR* 4.3 23.1 - - - +
1049L ASN* 5.4 3.5 + - - -
1256M ARG 4.3 2.4 - - - +
1257M PRO* 3.3 9.1 - - - +
1258M SER* 2.8 40.8 + - - +
1259M PHE 3.4 0.2 - - - -
1260M LEU* 1.3 76.4 - - + +
1262M ILE* 1.3 62.7 + - - +
1264M SER* 3.2 8.0 + - - -
1265M SER* 3.0 23.4 + - - -
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Residues in contact with ILE1262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986L VAL* 4.7 4.2 - - - +
1120M ALA* 4.7 6.3 - - + -
1195M VAL* 4.6 6.1 - - + -
1198M PHE* 3.7 39.0 - - + -
1244M LEU* 3.9 29.6 - - + -
1248M CYS* 3.9 17.7 - - - -
1257M PRO* 3.9 15.5 - - + -
1258M SER 2.9 25.0 + - - +
1259M PHE* 3.7 15.9 - - + +
1260M LEU 3.3 0.2 - - - -
1261M GLU* 1.3 73.7 - - - +
1263M ILE* 1.3 62.1 + - - +
1265M SER* 2.8 24.1 + - - -
1266M ILE* 3.5 13.0 + - + +
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Residues in contact with ILE1263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117M GLY* 4.3 3.4 - - - +
1120M ALA* 3.7 19.7 - - + +
1121M ASP* 3.5 39.7 - - + +
1124M ALA* 4.1 9.9 - - + -
1259M PHE 3.1 18.4 + - - +
1260M LEU* 3.8 1.3 - - + +
1262M ILE* 1.3 75.2 - - - +
1264M SER* 1.3 54.2 + - - +
1266M ILE* 2.9 13.6 + - + +
1267M LYS* 2.7 36.4 + - + -
1270M MET* 5.8 0.2 - - + -
1274M PHE* 3.9 27.4 - - + -
1280M TYR* 3.7 30.5 - - + -
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Residues in contact with SER1264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985L ASP 5.2 1.4 + - - -
986L VAL 5.3 2.5 + - - -
988L VAL 5.0 3.6 + - - -
989L PRO* 5.4 2.3 - - - +
990L ASP* 3.5 24.1 + - - +
1260M LEU 2.9 16.4 + - - -
1261M GLU* 3.5 8.7 + - - -
1263M ILE* 1.3 77.5 - - - +
1265M SER* 1.3 61.0 + - - +
1267M LYS* 3.4 26.4 + - - +
1268M GLU* 5.3 0.2 - - - +
1280M TYR* 3.3 26.4 + - - -
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Residues in contact with SER1265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981L PHE* 3.4 31.6 - - - -
985L ASP* 3.6 17.2 + - - +
986L VAL* 3.6 29.8 - - - +
990L ASP* 5.3 0.4 - - - -
1244M LEU* 4.9 3.3 - - - +
1261M GLU 3.0 5.2 + - - -
1262M ILE* 2.8 17.6 + - - -
1264M SER* 1.3 76.9 - - - +
1266M ILE* 1.3 64.6 + - - +
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Residues in contact with ILE1266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981L PHE* 4.7 0.7 - - + -
1113M ILE* 3.7 26.2 - - + +
1116M ALA* 4.3 8.7 - - + -
1117M GLY* 3.6 32.8 - - - +
1240M MET* 3.5 32.5 - - + -
1244M LEU* 4.8 4.9 - - + -
1262M ILE* 3.6 14.8 - - + +
1263M ILE* 2.9 15.8 + - + +
1265M SER* 1.3 90.5 - - - +
1267M LYS* 1.3 55.9 + - - +
1268M GLU 3.3 2.7 - - - -
1269M GLU* 2.7 35.0 + - + +
1270M MET* 3.5 9.6 + - - +
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Residues in contact with LYS1267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990L ASP* 4.3 15.7 + - - +
991L GLU* 5.6 3.8 + - - -
1263M ILE* 2.7 20.7 + - + +
1264M SER* 3.4 24.5 + - - +
1265M SER 3.7 0.4 - - - -
1266M ILE* 1.3 76.6 - - - +
1268M GLU* 1.3 81.4 + - - +
1269M GLU 3.1 4.5 + - - -
1270M MET* 3.2 27.4 + - - +
1274M PHE* 5.0 3.7 - - + +
1280M TYR* 3.6 30.5 + - + +
1281M TYR* 3.3 35.0 + - + +
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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