Contacts of the helix formed by residues 1011 - 1026 (chain B) in PDB entry 1OFD
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 SER1011 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B ASN* 5.2 1.6 - - - -
228B GLY* 6.1 2.0 - - - -
350B ARG* 3.1 21.4 + - - -
502B VAL 3.3 16.1 + - - +
503B THR 4.0 8.3 - - - -
1009B ILE* 3.5 4.5 - - - +
1010B TYR* 1.3 81.4 - - - +
1012B ILE* 1.3 66.1 + - - +
1013B GLU* 3.0 32.3 - - - -
1014B ASP* 3.2 8.8 + - - +
1015B LEU* 3.1 17.5 + - - +
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Residues in contact with ILE1012 (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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207B PHE* 3.7 48.2 - - + +
209B THR* 5.2 7.0 - - + -
502B VAL* 3.5 29.5 + - + -
503B THR* 4.4 15.5 + - + +
1011B SER* 1.3 71.8 - - - +
1013B GLU* 1.3 70.0 + - - +
1015B LEU* 3.2 13.6 + - + +
1016B ALA* 3.0 26.0 + - - +
1044B ILE 4.9 0.4 - - - +
1047B GLY* 3.4 33.2 - - - +
1048B VAL* 3.8 2.7 - - + +
1051B ALA* 4.0 2.0 - - + -
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Residues in contact with GLU1013 (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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1B CYS 3.1 24.3 + - - +
30B HIS 4.6 4.0 - - - +
31B ARG* 3.8 38.6 - - + +
207B PHE* 4.3 7.4 - - + -
227B ASN* 2.9 22.9 + - - -
350B ARG* 2.9 24.4 + - - +
1011B SER* 3.0 21.8 + - - +
1012B ILE* 1.3 83.8 - - - +
1014B ASP* 1.3 58.6 + - - +
1016B ALA* 3.4 9.6 + - - +
1017B GLN* 3.0 24.6 + - - +
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Residues in contact with ASP1014 (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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31B ARG* 4.4 7.1 + - - -
350B ARG* 2.8 36.9 + - - -
351B PRO* 5.7 0.5 - - - +
1008B ASP 3.3 23.8 - - - +
1009B ILE* 3.6 5.8 - - - -
1010B TYR* 3.0 17.5 + - - +
1011B SER* 3.2 15.3 + - - +
1013B GLU* 1.3 77.8 - - - +
1015B LEU* 1.3 65.1 + - - +
1017B GLN* 3.1 9.8 + - - +
1018B LEU* 3.0 19.2 + - - +
1311B GLN* 4.9 2.4 + - - -
1332B TYR* 3.6 20.1 + - - +
1335B LYS* 5.9 0.2 + - - -
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Residues in contact with LEU1015 (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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502B VAL* 3.8 28.3 - - + -
965B ILE* 3.9 28.3 - - + -
967B MET* 4.6 1.8 - - - -
1009B ILE* 3.9 33.7 - - + +
1011B SER 3.1 8.0 + - - +
1012B ILE* 3.4 15.7 - - + +
1014B ASP* 1.3 77.2 - - - +
1016B ALA* 1.3 56.5 + - - +
1018B LEU* 3.1 1.7 + - - -
1019B ILE* 2.9 53.2 + - + +
1033B VAL* 4.3 10.5 - - + -
1048B VAL* 3.8 21.8 - - + -
1051B ALA* 4.1 3.4 - - + -
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Residues in contact with ALA1016 (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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30B HIS 5.3 6.1 - - - +
207B PHE* 4.8 7.6 - - + -
1012B ILE 3.0 10.7 + - - +
1013B GLU* 3.4 13.7 - - - +
1015B LEU* 1.3 75.9 - - - +
1017B GLN* 1.3 58.4 + - - +
1019B ILE* 3.7 1.7 - - - +
1020B TYR* 2.8 29.9 + - - +
1051B ALA* 3.7 37.3 - - + +
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Residues in contact with GLN1017 (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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30B HIS* 4.8 4.3 - - - -
1013B GLU 3.0 14.0 + - - +
1014B ASP* 3.1 13.2 + - - +
1016B ALA* 1.3 76.4 - - - +
1018B LEU* 1.3 57.8 + - - +
1020B TYR* 3.2 12.8 + - - +
1021B ASP* 2.8 58.3 + - - +
1278B ARG* 3.5 25.5 + - - +
1279B THR* 3.2 12.3 + - - -
1311B GLN* 3.5 37.6 - - + +
1312B SER* 3.8 11.6 + - - +
1332B TYR* 4.3 11.7 - - + -
1335B LYS* 5.1 0.7 - - - +
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Residues in contact with LEU1018 (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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945B ILE* 4.5 9.2 - - + -
949B ARG* 3.8 19.1 - - - +
965B ILE* 3.7 28.7 - - + -
1008B ASP* 3.6 20.4 - - - +
1009B ILE* 3.7 30.1 - - + -
1014B ASP 3.0 12.9 + - - +
1015B LEU 3.1 6.9 + - - +
1017B GLN* 1.3 72.3 - - - +
1019B ILE* 1.3 67.4 + - - +
1021B ASP* 3.1 11.8 + - + +
1022B LEU* 3.0 37.3 + - + +
1316B PHE* 5.8 3.1 - - + -
1335B LYS* 3.9 14.1 - - + +
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Residues in contact with ILE1019 (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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965B ILE* 3.7 20.4 - - + -
1015B LEU* 2.9 40.3 + - + +
1016B ALA 3.7 4.9 - - - +
1018B LEU* 1.3 77.7 - - - +
1020B TYR* 1.3 63.3 + - - +
1022B LEU* 3.3 2.9 + - - +
1023B HIS* 3.0 37.2 + - + +
1031B VAL* 4.1 13.9 - - + +
1033B VAL* 4.1 4.0 - - + -
1051B ALA* 3.5 22.7 - - + +
1052B ASN* 3.7 21.5 - - + +
1053B ALA* 3.7 25.1 - - + +
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Residues in contact with TYR1020 (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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1016B ALA 2.8 15.6 + - - +
1017B GLN* 3.2 18.4 - - - +
1019B ILE* 1.3 78.6 - - - +
1021B ASP* 1.3 51.0 + - - +
1023B HIS* 4.9 0.2 - - - -
1024B GLN* 2.8 35.6 + - + +
1243B ASN* 2.9 54.1 + - + -
1245B PRO 5.1 0.2 + - - -
1246B VAL* 3.0 27.7 - - + +
1276B THR 4.9 1.6 + - - -
1278B ARG* 3.3 58.9 + - + +
1279B THR* 3.3 26.2 - - - -
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Residues in contact with ASP1021 (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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1017B GLN* 2.8 32.7 + - - +
1018B LEU* 3.1 13.6 + - + +
1020B TYR* 1.3 72.5 - - - +
1022B LEU* 1.3 60.1 + - + +
1024B GLN* 3.3 2.9 - - - +
1025B ILE* 3.1 28.2 + - - +
1279B THR* 2.6 42.4 + - + +
1282B THR* 4.2 3.5 - - - +
1312B SER* 2.9 21.0 + - - -
1315B ALA* 5.2 0.7 - - - -
1316B PHE* 5.0 13.4 - - + -
1335B LYS* 2.9 25.9 + - - -
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Residues in contact with LEU1022 (chain B).
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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945B ILE* 4.0 20.4 - - + -
957B LEU* 4.1 34.8 - - + -
963B LEU* 4.1 12.7 - - + +
965B ILE* 3.7 36.6 - - + -
1018B LEU* 3.0 28.1 + - + +
1019B ILE 3.8 3.6 - - - +
1021B ASP* 1.3 75.4 - - - +
1023B HIS* 1.3 65.6 + - - +
1024B GLN 3.1 1.1 - - - -
1025B ILE* 3.3 6.7 + - + +
1026B ASN* 3.0 27.0 + - - +
1031B VAL* 3.8 22.9 - - + -
1316B PHE* 5.0 6.5 - - + -
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Residues in contact with HIS1023 (chain B).
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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1019B ILE* 3.0 30.6 + - + +
1020B TYR* 4.8 0.4 - - - -
1022B LEU* 1.3 76.0 - - - +
1024B GLN* 1.3 62.5 + - - +
1026B ASN 4.0 4.9 + - - -
1027B PRO* 3.1 26.6 + - + +
1029B ALA 3.7 10.5 + - - -
1031B VAL* 3.7 12.4 - - + +
1052B ASN* 3.4 29.8 + - + -
1054B ASP* 2.9 26.0 + - - -
1240B VAL* 3.7 9.1 - - + +
1241B HIS* 3.5 28.0 + - - +
1243B ASN* 3.3 26.9 - - - +
1283B ARG* 3.1 8.5 + - - +
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Residues in contact with GLN1024 (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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1020B TYR* 2.8 20.4 + - - +
1021B ASP* 3.3 11.4 - - - +
1022B LEU 3.1 0.4 - - - -
1023B HIS* 1.3 77.2 - - - +
1025B ILE* 1.3 61.7 + - - +
1027B PRO* 3.9 0.7 - - - +
1243B ASN* 3.2 14.6 + - - +
1246B VAL* 3.6 34.6 - - - +
1248B ASP* 3.8 15.0 + - - +
1278B ARG 3.9 8.9 + - - -
1279B THR* 3.3 39.1 + - + +
1282B THR* 3.9 7.4 - - - -
1283B ARG* 3.0 45.0 + - - +
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Residues in contact with ILE1025 (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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954B PRO* 4.0 29.6 - - + +
957B LEU* 4.1 24.5 - - + -
958B MET* 3.4 17.3 - - - +
963B LEU* 5.1 0.9 - - + -
1021B ASP 3.1 13.6 + - - +
1022B LEU* 3.4 14.4 - - + +
1024B GLN* 1.3 76.9 - - - +
1026B ASN* 1.3 67.7 + - + +
1027B PRO* 3.6 4.6 - - - +
1282B THR* 3.7 22.6 - - + +
1283B ARG* 4.6 2.3 - - - +
1285B SER* 5.0 0.4 - - - -
1286B GLY* 3.5 27.9 - - - +
1316B PHE* 3.8 32.8 - - + -
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Residues in contact with ASN1026 (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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957B LEU 3.1 24.0 + - - +
958B MET* 3.8 28.2 + - - +
960B GLY 3.4 18.4 + - - -
963B LEU* 4.4 2.7 - - + -
1022B LEU 3.0 14.9 + - - +
1023B HIS* 3.5 4.0 - - - +
1025B ILE* 1.3 83.5 - - + +
1027B PRO* 1.3 63.5 - - - +
1028B GLU* 3.1 16.5 + - - +
1029B ALA* 3.1 33.4 + - + +
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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