Contacts of the helix formed by residues 1203 - 1210 (chain A) in PDB entry 1FP7
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 SER1203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1136A VAL* 4.5 5.6 - - - -
1140A HIS* 2.5 39.8 - - - +
1169A VAL* 4.3 10.5 - - - +
1198A ASP* 6.0 0.9 - - - -
1199A ILE 3.9 0.8 + - - -
1200A SER* 2.5 25.9 + - - -
1201A VAL 4.3 0.5 - - - +
1202A ALA* 1.3 71.9 - - - +
1204A GLU* 1.3 57.8 + - - +
1205A VAL* 2.9 17.4 + - - +
1206A MET* 2.9 27.0 + - - +
1207A ALA* 3.4 4.5 + - - +
1274A PRO* 5.8 0.3 - - - +
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Residues in contact with GLU1204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140A HIS* 4.7 0.6 + - - -
1166A TRP* 4.0 23.7 - - + -
1202A ALA 3.5 4.1 + - - -
1203A SER* 1.3 72.6 + - - +
1205A VAL* 1.3 56.5 + - - +
1207A ALA* 3.1 11.1 + - + +
1208A CYS* 3.1 34.0 + - - -
1225A ILE* 4.6 19.1 - - + +
1518A LEU 4.0 4.9 - - - +
1519A SER* 3.2 34.6 + - - +
1520A ALA 3.3 1.6 + - - -
1521A GLY* 2.8 34.6 + - - +
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Residues in contact with VAL1205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136A VAL* 3.3 30.7 - - + +
1139A ALA* 4.3 5.2 - - + -
1140A HIS* 3.9 10.3 - - + +
1166A TRP* 3.7 25.1 - - + -
1203A SER* 2.9 12.8 - - - +
1204A GLU* 1.3 76.6 - - - +
1206A MET* 1.3 60.6 + - - +
1208A CYS* 3.7 2.9 + - - +
1209A LEU* 3.2 21.1 + - - +
1222A PHE* 4.0 25.8 - - + -
1225A ILE* 5.5 1.1 - - + -
1247A MET* 3.9 22.0 - - + -
1251A MET* 4.2 8.3 - - + +
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Residues in contact with MET1206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132A ASP* 4.9 1.3 - - + +
1133A ILE* 4.5 23.3 - - + +
1136A VAL* 3.3 41.4 - - + +
1200A SER 4.1 4.3 - - - +
1201A VAL* 3.6 22.9 - - + +
1203A SER 2.9 11.9 + - - +
1205A VAL* 1.3 78.4 - - - +
1207A ALA* 1.3 63.1 + - - +
1209A LEU* 3.5 10.2 - - + +
1210A CYS* 3.3 22.9 + - - -
1272A GLY* 4.0 10.3 - - - -
1273A GLY 3.4 44.2 - - - +
1274A PRO* 4.1 2.5 - - + -
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Residues in contact with ALA1207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203A SER 3.4 2.9 + - - +
1204A GLU* 3.1 22.3 + - + +
1206A MET* 1.3 77.5 - - - +
1208A CYS* 1.3 66.6 + - - +
1210A CYS* 3.1 13.5 + - - +
1211A LEU* 3.2 20.4 + - + +
1274A PRO* 4.7 5.3 - - + +
1278A ILE 5.8 0.4 - - - +
1279A ALA* 4.7 11.4 - - + -
1280A HIS* 4.6 8.3 - - + -
1519A SER* 6.3 1.3 - - - -
1521A GLY 4.9 4.7 - - - +
1523A ARG* 4.5 18.4 - - - +
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Residues in contact with CYS1208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204A GLU* 3.1 21.0 + - - +
1205A VAL 4.0 4.3 - - - +
1207A ALA* 1.3 77.9 - - - +
1209A LEU* 1.3 57.8 + - - +
1211A LEU* 2.9 4.5 + - - +
1212A ALA* 2.6 35.3 + - - +
1218A LEU* 3.9 16.2 - - + -
1221A ARG* 4.2 20.2 - - - +
1222A PHE* 4.2 16.4 - - + -
1521A GLY* 3.3 36.3 - - - -
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Residues in contact with LEU1209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132A ASP* 5.2 5.8 - - + -
1136A VAL* 4.3 12.8 - - + -
1205A VAL 3.2 13.1 + - - +
1206A MET* 3.5 15.3 - - + +
1207A ALA 3.2 0.2 - - - -
1208A CYS* 1.3 81.0 - - - +
1210A CYS* 1.3 57.2 + - - +
1211A LEU 3.2 2.9 + - - -
1212A ALA* 3.7 10.7 + - - +
1218A LEU* 3.9 7.7 - - + +
1251A MET* 3.5 26.0 - - + -
1254A ALA* 3.5 25.4 - - + +
1255A ILE* 4.1 19.4 - - + +
1271A HIS* 4.0 26.1 - - + +
1272A GLY* 4.3 14.1 - - - -
1284A SER* 4.1 8.0 - - - -
1286A ILE* 4.8 4.3 - - - +
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Residues in contact with CYS1210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206A MET 3.3 14.1 + - - +
1207A ALA 3.1 7.2 + - - +
1209A LEU* 1.3 77.8 - - - +
1211A LEU* 1.3 63.0 + - - +
1272A GLY* 3.4 14.4 - - - -
1273A GLY 3.1 32.1 - - - -
1274A PRO* 3.7 10.3 - - - -
1280A HIS* 3.5 24.5 + - + +
1282A CYS 3.8 4.7 - - - +
1283A ASN 3.6 2.1 - - - +
1284A SER* 3.4 19.7 - - - +
1285A ILE* 3.2 20.2 + - - +
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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