Contacts of the helix formed by residues 1258 - 1267 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1191H THR* 6.0 1.8 - - - -
1195H VAL* 4.5 2.7 - - - -
1256H ARG 4.0 0.2 + - - -
1257H PRO* 1.3 77.2 - - - +
1259H PHE* 1.3 63.7 + - - +
1260H LEU* 3.3 10.6 + - - +
1261H GLU* 3.0 38.3 + - - +
1262H ILE* 3.1 22.6 + - - +
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Residues in contact with PHE1259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120H ALA* 3.7 22.8 - - + +
1123H MET* 3.5 55.6 - - + -
1124H ALA* 3.8 11.2 - - + -
1127H ASN* 3.2 28.7 - - + -
1191H THR* 5.8 0.2 - - - -
1194H ASP* 3.8 6.7 - - + -
1195H VAL* 3.7 33.4 - - + +
1198H PHE* 3.7 28.0 - + + -
1258H SER* 1.3 73.2 - - - +
1260H LEU* 1.3 62.7 + - - +
1262H ILE* 3.2 14.9 + - + +
1263H ILE* 3.0 28.0 + - - +
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Residues in contact with LEU1260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124H ALA* 3.8 23.3 - - + +
1258H SER* 3.2 9.5 + - - +
1259H PHE* 1.3 77.5 - - - +
1261H GLU* 1.3 58.0 + - + +
1263H ILE* 3.3 6.0 + - + +
1264H SER* 2.9 28.1 + - - -
1279H PHE* 4.3 7.2 - - + -
1280H TYR* 3.7 21.7 - - + -
1285H ASN* 3.5 38.8 - - - +
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Residues in contact with GLU1261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986C VAL* 3.7 28.1 - - + +
987C TYR* 4.3 21.7 - - - +
989C PRO* 5.2 6.8 - - + +
1256H ARG 4.6 1.2 - - - +
1257H PRO* 3.5 8.7 - - - +
1258H SER* 3.0 39.8 + - - +
1260H LEU* 1.3 74.8 - - + +
1262H ILE* 1.3 65.3 + - - +
1264H SER* 3.4 10.1 + - - +
1265H SER* 3.2 22.7 + - - -
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Residues in contact with ILE1262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986C VAL* 4.8 2.5 - - + -
1120H ALA* 4.4 7.4 - - + -
1195H VAL* 4.4 6.1 - - + -
1198H PHE* 3.7 44.4 - - + -
1244H LEU* 4.1 25.4 - - + -
1248H CYS* 4.0 13.0 - - - -
1257H PRO* 3.9 17.7 - - + -
1258H SER 3.1 17.4 + - - +
1259H PHE* 3.5 18.2 - - + +
1261H GLU* 1.3 77.7 - - - +
1263H ILE* 1.3 61.7 + - - +
1265H SER* 2.6 24.3 + - - -
1266H ILE* 3.3 12.9 - - + +
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Residues in contact with ILE1263 (chain H).
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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1117H GLY* 4.2 6.3 - - - +
1120H ALA* 3.6 23.8 - - + +
1121H ASP* 3.5 40.2 - - + +
1124H ALA* 4.2 9.9 - - + -
1259H PHE 3.0 14.7 + - - +
1260H LEU 3.7 5.6 - - - +
1261H GLU 3.3 0.2 - - - -
1262H ILE* 1.3 77.6 - - - +
1264H SER* 1.3 58.3 + - - +
1265H SER 3.0 0.5 + - - -
1266H ILE* 3.1 8.3 + - + -
1267H LYS* 2.8 30.8 + - + +
1270H MET* 5.9 0.7 - - + -
1274H PHE* 3.9 18.4 - - + -
1280H TYR* 3.4 36.6 - - + -
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Residues in contact with SER1264 (chain H).
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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985C ASP 4.9 1.6 + - - -
986C VAL 4.7 5.0 + - - -
988C VAL 5.3 1.4 + - - -
989C PRO* 5.5 2.5 - - - +
990C ASP* 4.1 20.0 + - - +
1260H LEU 2.9 15.9 + - - -
1261H GLU* 3.5 10.3 + - - -
1262H ILE 3.4 0.4 - - - -
1263H ILE* 1.3 76.8 - - - +
1265H SER* 1.3 63.1 + - - +
1266H ILE 3.6 0.2 + - - -
1267H LYS* 3.2 29.3 + - - +
1268H GLU* 5.9 0.3 - - - +
1280H TYR* 3.4 25.1 - - - -
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Residues in contact with SER1265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981C PHE* 3.8 23.6 - - - -
985C ASP* 4.0 10.3 - - - +
986C VAL* 3.8 25.3 - - - +
990C ASP* 5.1 1.6 - - - -
1244H LEU* 5.0 2.6 - - - +
1261H GLU 3.2 10.9 + - - -
1262H ILE* 2.6 25.1 + - - +
1264H SER* 1.3 82.2 + - - +
1266H ILE* 1.3 68.2 + - - +
1268H GLU* 5.4 1.1 + - - +
1269H GLU* 4.9 3.3 - - - +
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Residues in contact with ILE1266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981C PHE* 4.5 2.7 - - + -
1113H ILE* 3.9 26.9 - - + +
1116H ALA* 4.4 8.1 - - + -
1117H GLY* 3.7 34.3 - - - +
1240H MET* 4.1 25.8 - - + -
1244H LEU* 4.7 5.4 - - + -
1262H ILE* 3.3 22.4 - - + +
1263H ILE* 3.7 6.5 - - + +
1265H SER* 1.3 90.7 - - - +
1267H LYS* 1.3 68.1 + - - +
1268H GLU 3.1 2.9 - - - -
1269H GLU* 3.0 22.9 + - - +
1270H MET* 3.6 11.4 + - - +
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Residues in contact with LYS1267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990C ASP* 5.1 13.8 - - - +
1263H ILE* 2.8 22.4 + - + +
1264H SER* 3.2 25.8 + - - +
1265H SER 3.7 0.2 - - - -
1266H ILE* 1.3 77.8 - - - +
1268H GLU* 1.3 80.6 + - + +
1270H MET* 3.1 29.7 + - + +
1274H PHE* 5.2 2.2 - - + -
1280H TYR* 3.2 27.6 + - + +
1281H TYR* 3.3 35.2 + - + +
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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