Contacts of the helix formed by residues 1110 - 1120 (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 THR1110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827B TYR* 5.3 0.2 + - - -
830B TYR* 4.9 1.0 + - - -
831B ARG* 2.8 34.0 + - - +
834B LEU* 3.7 16.1 - - - +
837B ARG* 6.2 0.7 - - - +
1109B LYS* 1.3 81.4 + - - +
1111B GLY* 1.3 62.9 + - - +
1112B TRP* 3.1 31.4 - - + +
1113B ASP* 3.1 35.1 + - - +
1114B VAL* 3.1 16.1 + - - +
1127B PHE* 4.7 0.8 - - - -
1177B ILE* 4.0 10.5 - - - -
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Residues in contact with GLY1111 (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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1110B THR* 1.3 72.6 - - - +
1112B TRP* 1.3 56.8 + - - +
1114B VAL* 3.3 3.3 + - - +
1115B VAL* 3.0 32.4 + - - +
1177B ILE* 3.7 23.6 - - - +
1180B GLU* 3.4 24.4 + - - +
1181B VAL* 3.8 9.1 - - - +
1184B LEU* 3.8 6.7 - - - -
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Residues in contact with TRP1112 (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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831B ARG* 4.4 4.5 - - - +
837B ARG* 3.9 16.4 - - - -
843B ARG* 3.4 55.2 - - + -
844B ASP* 3.6 18.4 - - - -
846B LEU 4.1 11.8 + - - -
847B ASP* 5.2 5.3 + - - +
848B PHE* 3.7 35.9 - + - -
1110B THR* 3.1 12.5 - - + +
1111B GLY* 1.3 73.3 - - - +
1113B ASP* 1.3 78.0 + - - +
1115B VAL* 3.3 1.9 + - - +
1116B MET* 3.0 46.8 + - + +
1180B GLU* 3.1 12.3 + - - +
1184B LEU* 3.6 15.4 - - + +
1206B ARG* 5.9 2.7 - - - -
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Residues in contact with ASP1113 (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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796B MET* 6.1 0.3 - - - +
837B ARG* 4.7 5.0 + - - -
843B ARG* 3.2 26.6 + - - +
1080B TRP* 4.3 1.7 - - - -
1107B GLY 3.8 4.6 - - - +
1108B LEU* 4.0 22.5 - - + +
1109B LYS* 3.0 28.0 + - - +
1110B THR* 3.1 27.1 + - - +
1112B TRP* 1.3 95.6 - - - +
1114B VAL* 1.3 55.6 + - - +
1116B MET* 3.5 5.6 + - - +
1117B ALA* 3.0 28.9 + - - +
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Residues in contact with VAL1114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870B PHE* 4.1 13.7 - - + -
1108B LEU* 5.5 2.5 - - + -
1110B THR 3.1 13.6 + - - +
1111B GLY 3.3 7.4 + - - +
1113B ASP* 1.3 77.1 - - + +
1115B VAL* 1.3 57.7 + - - +
1117B ALA* 3.2 7.3 + - - +
1118B ALA* 2.9 27.0 + - - +
1125B TYR* 3.7 36.8 - - + -
1127B PHE* 3.8 28.5 - - + -
1177B ILE* 4.2 7.0 - - + -
1181B VAL* 3.9 17.9 - - + -
1193B LEU* 4.4 9.2 - - + -
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Residues in contact with VAL1115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B PHE* 3.8 26.5 - - + -
1111B GLY 3.0 19.8 + - - +
1112B TRP 3.9 4.0 - - - +
1114B VAL* 1.3 75.5 - - - +
1116B MET* 1.3 58.1 + - - +
1118B ALA* 3.3 7.3 + - - +
1119B LEU* 2.9 32.7 + - + +
1181B VAL* 4.4 21.3 - - + +
1184B LEU* 3.7 27.6 - - + -
1185B LEU* 5.3 2.0 - - + +
1188B LEU* 4.2 10.1 - - + -
1193B LEU* 4.6 6.5 - - + -
1196B ILE* 3.9 17.0 - - + -
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Residues in contact with MET1116 (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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843B ARG* 3.6 28.9 - - + +
846B LEU* 3.6 27.6 - - + +
847B ASP* 5.9 0.2 - - - -
848B PHE* 4.0 15.3 - - + -
1080B TRP* 4.2 5.4 - - + -
1112B TRP* 3.0 48.4 + - + +
1113B ASP 3.6 5.8 - - - +
1115B VAL* 1.3 74.0 - - - +
1117B ALA* 1.3 64.2 + - - +
1119B LEU* 3.4 3.3 + - - +
1120B MET* 3.1 54.7 + - + +
1203B LEU* 3.5 21.5 - - + -
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Residues in contact with ALA1117 (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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1080B TRP* 3.6 26.2 - - + -
1084B VAL* 4.3 0.9 - - - +
1104B ALA* 4.7 6.3 - - + -
1108B LEU* 4.8 5.2 - - + -
1113B ASP 3.0 17.8 + - - +
1114B VAL* 3.5 5.6 - - - +
1116B MET* 1.3 76.3 - - - +
1118B ALA* 1.3 61.6 + - - +
1120B MET* 3.3 4.5 + - - +
1121B GLY 3.2 6.6 + - - -
1122B ALA* 2.9 30.0 + - + +
1125B TYR* 3.9 19.3 - - + -
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Residues in contact with ALA1118 (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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1114B VAL 2.9 14.1 + - - +
1115B VAL* 3.5 6.1 - - - +
1116B MET 3.3 0.2 - - - -
1117B ALA* 1.3 74.3 - - - +
1119B LEU* 1.3 61.7 + - - +
1121B GLY 2.9 7.4 + - - -
1122B ALA 3.3 12.6 - - - +
1125B TYR* 3.3 19.0 - - - +
1193B LEU* 4.1 17.5 - - + -
1196B ILE* 4.3 5.6 - - + -
1197B ILE* 3.3 17.1 - - + +
1198B GLY 2.9 22.4 + - - -
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Residues in contact with LEU1119 (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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848B PHE* 3.6 35.4 - - + -
1115B VAL* 2.9 23.7 + - + +
1116B MET* 3.9 4.9 - - - +
1118B ALA* 1.3 76.5 - - - +
1120B MET* 1.3 57.8 + - - +
1188B LEU* 5.1 2.7 - - + -
1196B ILE* 3.5 31.2 - - + +
1198B GLY* 3.2 24.9 - - - +
1199B ARG 3.3 22.2 - - - +
1200B THR* 3.7 10.4 + - - -
1202B LEU* 3.9 21.5 - - + -
1203B LEU* 3.7 27.8 - - + -
1225B LEU* 4.6 0.2 - - - +
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Residues in contact with MET1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843B ARG* 4.3 1.3 - - + -
846B LEU* 3.9 16.2 - - + -
1080B TRP* 4.0 10.3 - - + -
1081B GLU* 3.8 44.0 - - + +
1084B VAL* 3.5 20.3 - - + +
1085B THR* 3.8 16.9 - - - +
1088B HIS* 3.8 7.1 - - - +
1116B MET* 3.1 48.5 + - + +
1117B ALA 3.7 5.4 - - - +
1118B ALA 3.2 0.6 - - - -
1119B LEU* 1.3 76.8 - - - +
1121B GLY* 1.3 55.5 + - - +
1198B GLY* 4.7 0.2 - - - -
1200B THR* 4.9 0.2 - - - -
1203B LEU* 4.4 11.2 - - + -
1222B LEU* 4.4 9.4 - - + +
1225B LEU* 3.7 21.6 - - - +
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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