Contacts of the helix formed by residues 1203 - 1211 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1136B VAL* 3.9 5.8 - - - +
1140B HIS* 2.7 38.4 - - - -
1169B VAL* 4.8 1.3 - - - -
1198B ASP* 6.3 0.4 - - - -
1199B ILE 4.0 0.9 + - - -
1200B SER* 2.9 21.2 + - - -
1201B VAL 3.0 3.2 - - - +
1202B ALA* 1.3 81.6 - - - +
1204B GLU* 1.3 60.7 + - - +
1205B VAL* 2.8 26.1 + - - +
1206B MET* 3.3 20.1 - - - +
1207B ALA* 3.5 5.9 + - - +
1274B PRO* 5.3 1.6 - - - +
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Residues in contact with GLU1204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140B HIS* 4.5 3.8 + - - -
1166B TRP* 3.8 19.7 - - + -
1202B ALA 3.9 0.6 + - - -
1203B SER* 1.3 71.0 + - - +
1205B VAL* 1.3 54.3 + - - +
1206B MET 2.7 14.4 + - - -
1207B ALA* 2.9 10.3 + - + +
1208B CYS* 2.9 36.5 + - - -
1225B ILE* 3.8 23.6 - - + +
1518B LEU 5.2 0.3 - - - +
1519B SER* 3.1 35.0 + - - +
1520B ALA 3.3 1.3 + - - -
1521B GLY* 2.8 36.3 + - - +
1523B ARG* 5.3 2.5 - - - +
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Residues in contact with VAL1205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136B VAL* 3.0 38.4 - - + +
1139B ALA* 4.0 11.2 - - + -
1140B HIS* 4.0 12.3 - - + -
1166B TRP* 3.7 30.3 - - + -
1203B SER* 2.8 10.3 + - - +
1204B GLU* 1.3 75.5 - - - +
1206B MET* 1.3 54.8 + - - -
1208B CYS* 4.7 1.1 - - - -
1209B LEU* 4.1 10.2 + - - +
1222B PHE* 3.9 31.1 - - + -
1225B ILE* 4.6 4.0 - - + -
1247B MET* 4.1 12.8 - - + -
1251B MET* 4.5 4.1 - - - +
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Residues in contact with MET1206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098B GLU* 5.1 4.0 - - + +
1133B ILE* 5.2 9.4 - - + -
1136B VAL* 4.1 13.0 - - + -
1200B SER 4.4 0.7 - - - +
1201B VAL* 3.5 35.4 - - + +
1203B SER* 3.3 21.1 + - - +
1204B GLU 2.7 0.2 - - - -
1205B VAL* 1.3 81.2 - - - +
1207B ALA* 1.3 69.6 + - - +
1208B CYS 3.3 0.9 - - - -
1209B LEU* 2.9 35.5 - - + +
1210B CYS* 3.0 6.9 + - - -
1272B GLY* 3.8 7.4 - - - -
1273B GLY 2.9 45.5 - - - +
1274B PRO* 4.1 7.9 - - + -
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Residues in contact with ALA1207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203B SER 3.5 4.4 + - - +
1204B GLU* 2.9 20.2 + - + +
1206B MET* 1.3 78.4 - - - +
1208B CYS* 1.3 57.2 + - - +
1210B CYS* 2.6 30.7 + - - +
1211B LEU* 2.9 21.7 + - + +
1274B PRO* 4.7 9.8 - - + +
1279B ALA* 5.0 6.5 - - + -
1280B HIS* 4.8 4.0 - - + -
1521B GLY 5.1 3.1 - - - +
1522B GLY* 6.5 0.2 - - - -
1523B ARG* 4.2 24.2 - - - +
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Residues in contact with CYS1208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204B GLU* 2.9 21.3 + - - +
1205B VAL* 4.7 0.7 - - - -
1207B ALA* 1.3 78.5 - - - +
1209B LEU* 1.3 63.3 + - - +
1211B LEU* 3.4 4.0 - - - +
1212B ALA* 3.0 31.0 + - - +
1218B LEU* 3.7 5.6 - - + -
1221B ARG* 4.1 20.9 - - - +
1222B PHE* 4.1 30.5 - - + -
1225B ILE* 6.3 2.2 - - - -
1521B GLY* 3.2 38.3 + - - -
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Residues in contact with LEU1209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132B ASP* 5.6 5.8 - - + +
1136B VAL* 4.0 23.6 - - + -
1205B VAL 4.1 5.9 + - - +
1206B MET* 2.9 33.9 + - + +
1207B ALA 2.8 1.6 + - - -
1208B CYS* 1.3 80.1 - - - +
1210B CYS* 1.3 60.5 + - - +
1211B LEU 3.1 1.2 + - - -
1212B ALA* 3.6 9.9 + - - +
1218B LEU* 4.0 7.7 - - + +
1251B MET* 3.4 23.1 - - + -
1254B ALA* 4.2 19.3 - - + +
1255B ILE* 4.4 16.6 - - + +
1271B HIS* 4.3 18.4 - - + +
1272B GLY* 4.6 13.2 - - - +
1284B SER* 4.5 5.0 - - - -
1285B ILE 4.9 0.3 + - - -
1286B ILE* 5.0 4.9 - - - +
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Residues in contact with CYS1210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206B MET* 3.0 11.6 + - - +
1207B ALA 2.6 12.1 + - - +
1209B LEU* 1.3 76.8 - - - +
1211B LEU* 1.3 58.1 + - - +
1272B GLY* 4.0 9.9 - - - -
1273B GLY 3.3 30.7 - - - -
1274B PRO* 3.4 17.7 - - - -
1280B HIS* 3.9 10.8 - - + +
1282B CYS 3.6 8.3 - - - +
1283B ASN 3.7 15.3 - - - +
1284B SER* 3.5 9.8 - - - +
1285B ILE* 2.7 31.8 + - - +
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Residues in contact with LEU1211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207B ALA* 2.9 22.3 + - + +
1208B CYS* 3.4 5.4 - - - +
1209B LEU 3.1 0.2 - - - -
1210B CYS* 1.3 79.8 - - - +
1212B ALA* 1.3 58.0 + - - +
1217B ASP* 4.6 0.2 - - - +
1221B ARG* 3.1 25.6 + - - +
1280B HIS* 3.1 44.2 - - + +
1285B ILE* 3.8 30.5 - - + +
1316B VAL* 3.5 23.8 - - + -
1317B LYS* 4.3 3.1 - - + -
1320B TYR* 4.4 19.0 - - + -
1521B GLY 5.4 1.6 - - - +
1522B GLY* 5.3 8.5 - - - -
1523B ARG* 5.2 11.0 - - + +
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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