Contacts of the helix formed by residues 1040 - 1051 (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 GLY1040 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498B ARG* 4.4 6.1 - - - -
1038B GLU* 5.3 0.2 - - - -
1039B ILE* 1.3 79.4 - - - +
1041B ILE* 1.3 64.1 + - - +
1042B GLY 3.1 2.6 + - - -
1043B THR* 3.5 11.9 + - - -
1044B ILE* 3.2 30.8 + - - +
1086B GLU* 2.9 12.7 + - - -
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Residues in contact with ILE1041 (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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501B GLN* 4.2 9.6 - - - +
1035B LEU* 3.8 30.3 - - + -
1036B VAL 3.6 23.6 - - - +
1037B ALA* 3.9 4.7 - - - -
1038B GLU* 3.0 23.5 + - - +
1039B ILE 3.4 0.2 - - - -
1040B GLY* 1.3 77.8 - - - +
1042B GLY* 1.3 59.1 + - - +
1044B ILE* 3.8 8.5 - - - +
1045B ALA* 2.8 29.3 + - - +
1058B ILE* 4.0 15.7 - - + -
1083B GLY* 4.0 14.4 - - - +
1086B GLU* 3.7 13.2 - - - +
1087B VAL* 3.8 25.6 - - + -
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Residues in contact with GLY1042 (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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1041B ILE* 1.3 78.7 - - - +
1043B THR* 1.3 61.4 + - - +
1045B ALA* 3.2 4.0 + - - +
1046B ALA 3.0 19.8 + - - -
1086B GLU* 2.9 30.4 + - - -
1087B VAL* 4.3 6.5 - - - -
1090B VAL* 3.4 29.0 - - - +
1091B LEU* 5.5 0.2 - - - +
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Residues in contact with THR1043 (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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209B THR* 3.0 39.2 - - + +
503B THR* 5.8 2.5 - - + -
1040B GLY* 3.5 12.7 + - - -
1042B GLY* 1.3 72.6 - - - +
1044B ILE* 1.3 66.1 + - + +
1046B ALA* 3.3 4.2 + - - +
1047B GLY 3.2 15.6 + - - -
1086B GLU* 4.6 0.8 + - - -
1090B VAL* 4.1 9.1 - - - +
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Residues in contact with ILE1044 (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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498B ARG* 5.4 4.7 - - - +
501B GLN* 3.5 43.1 - - + +
502B VAL* 3.8 22.4 - - + -
503B THR* 3.7 29.1 - - + +
1012B ILE* 4.9 1.2 - - - +
1035B LEU* 4.1 12.8 - - + -
1038B GLU* 4.6 5.4 - - - +
1040B GLY* 3.2 21.8 + - - +
1041B ILE* 3.7 9.9 - - - +
1043B THR* 1.3 79.4 - - + +
1045B ALA* 1.3 57.7 + - - +
1047B GLY* 3.0 5.4 + - - -
1048B VAL* 2.9 28.6 + - + +
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Residues in contact with ALA1045 (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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1035B LEU* 4.5 7.2 - - + -
1041B ILE 2.8 20.7 + - - +
1042B GLY 3.6 4.5 - - - +
1044B ILE* 1.3 73.7 - - - +
1046B ALA* 1.3 58.0 + - - +
1048B VAL* 3.1 6.1 + - - +
1049B ALA* 2.8 27.5 + - - +
1056B ILE* 3.5 20.0 - - + +
1087B VAL* 3.6 35.0 - - + -
1091B LEU* 3.8 5.1 - - + +
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Residues in contact with ALA1046 (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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209B THR 3.2 23.3 - - - +
1042B GLY 3.0 13.5 + - - +
1043B THR 3.6 4.7 - - - +
1044B ILE 3.2 0.2 - - - -
1045B ALA* 1.3 76.4 - - - +
1047B GLY* 1.3 61.2 + - - +
1049B ALA 3.4 0.9 + - - -
1050B LYS* 3.1 28.4 + - - +
1090B VAL* 4.2 14.1 - - + -
1091B LEU* 3.8 12.7 - - + +
1094B ASN* 4.3 3.6 - - - +
1096B LEU* 3.7 17.4 - - + +
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Residues in contact with GLY1047 (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* 4.6 1.6 - - - -
209B THR* 4.1 20.0 - - - -
503B THR* 6.2 0.2 - - - -
1012B ILE* 3.4 23.3 - - - +
1043B THR 3.2 7.5 + - - -
1044B ILE 3.0 8.0 + - - -
1046B ALA* 1.3 74.5 - - - +
1048B VAL* 1.3 57.3 + - - +
1050B LYS* 3.1 9.6 + - - +
1051B ALA* 2.8 29.1 + - - +
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Residues in contact with VAL1048 (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* 4.2 11.2 - - + -
1012B ILE* 4.2 0.2 - - - -
1015B LEU* 3.8 18.2 - - + -
1033B VAL* 3.8 21.3 - - + -
1035B LEU* 4.5 4.0 - - + -
1044B ILE* 2.9 31.8 + - + +
1045B ALA* 3.1 8.7 + - - +
1047B GLY* 1.3 75.5 - - - +
1049B ALA* 1.3 62.1 + - - +
1051B ALA* 3.0 21.7 + - - +
1053B ALA* 3.5 28.1 + - + -
1056B ILE* 3.6 24.7 - - + -
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Residues in contact with ALA1049 (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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1045B ALA 2.8 19.3 + - - +
1046B ALA 3.7 4.5 - - - +
1047B GLY 3.3 0.2 - - - -
1048B VAL* 1.3 72.0 - - - +
1050B LYS* 1.3 63.3 + - - +
1052B ASN* 3.2 15.4 + - - -
1053B ALA 4.3 1.5 + - - +
1056B ILE* 4.3 0.6 - - - +
1091B LEU* 3.9 18.4 - - + -
1096B LEU* 4.2 18.8 - - + +
1099B ARG* 4.3 20.7 + - + +
1100B VAL* 4.2 24.5 - - + -
1241B HIS* 5.9 0.2 - - - -
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Residues in contact with LYS1050 (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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33B GLY* 4.5 0.9 - - - -
34B CYS 3.2 23.8 + - - +
42B ASP* 2.8 36.0 + - - -
207B PHE* 4.0 19.4 - - + -
208B SER 3.0 17.7 + - - +
210B ASN 2.8 32.1 + - - +
211B THR* 4.7 2.5 - - - +
1046B ALA 3.1 16.0 + - - +
1047B GLY 3.5 7.2 - - - +
1049B ALA* 1.3 74.6 - - - +
1051B ALA* 1.3 56.3 + - - +
1052B ASN* 3.2 4.9 + - - +
1096B LEU* 4.1 24.7 - - + -
1099B ARG* 4.7 11.3 + - - +
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Residues in contact with ALA1051 (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* 4.5 2.2 - - + -
1012B ILE* 4.0 17.0 - - + +
1015B LEU* 4.1 2.0 - - + -
1016B ALA* 3.7 37.1 - - + +
1019B ILE* 3.5 22.4 - - + +
1047B GLY 2.8 11.6 + - - +
1048B VAL 3.0 11.7 + - - +
1050B LYS* 1.3 75.8 - - - +
1052B ASN* 1.3 66.6 + - - +
1053B ALA 3.4 1.6 - - - -
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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