Contacts of the helix formed by residues 1128 - 1135 (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 GLY1128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872B THR 4.1 2.2 - - - -
875B MET* 3.7 23.2 - - - +
1127B PHE* 1.3 71.9 - - - +
1129B SER* 1.3 65.1 + - - -
1130B ILE* 3.3 1.3 - - - +
1131B ALA* 3.0 15.9 + - - +
1132B MET* 3.2 13.3 + - - +
3508B FMN 2.8 32.7 + - - -
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Residues in contact with SER1129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B MET* 3.2 38.6 - - - +
476B GLY 5.2 0.5 + - - -
797B ASN* 4.6 14.3 + - - -
875B MET* 4.6 0.2 - - - -
1064B GLY* 3.7 8.1 + - - -
1128B GLY* 1.3 70.3 - - - +
1130B ILE* 1.3 62.1 + - - +
1132B MET* 3.1 14.0 + - - +
1133B ILE* 2.9 31.7 + - - +
1137B CYS* 5.2 0.2 - - - +
3508B FMN 2.7 33.5 + - - +
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Residues in contact with ILE1130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ASN* 5.3 1.3 - - - +
801B MET* 6.2 1.1 - - - -
805B LEU* 4.1 12.7 - - + +
830B TYR* 4.4 4.9 - - + +
1107B GLY* 4.7 1.6 - - - -
1108B LEU 2.6 32.1 - - - +
1109B LYS* 3.5 29.2 - - + -
1127B PHE* 4.5 5.4 - - + -
1128B GLY 4.0 5.4 - - - +
1129B SER* 1.3 77.4 - - - +
1131B ALA* 1.3 57.8 + - - +
1133B ILE* 3.3 13.3 + - + +
1134B ALA* 3.0 26.2 + - - +
1173B PHE* 3.7 33.3 - - + -
3508B FMN 3.0 32.1 - - - +
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Residues in contact with ALA1131 (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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872B THR* 3.5 24.7 - - - +
888B LEU* 4.0 18.1 - - + +
1127B PHE* 4.0 10.3 - - - +
1128B GLY* 3.0 12.0 + - - +
1130B ILE* 1.3 75.2 - - - +
1132B MET* 1.3 65.3 + - - +
1134B ALA* 3.3 9.8 + - - +
1135B GLU* 3.2 24.8 + - - +
1170B VAL* 4.7 0.8 - - + +
1173B PHE* 5.1 2.7 - - - -
1174B PHE* 4.6 15.9 - - + -
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Residues in contact with MET1132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B MET* 4.9 8.1 - - - +
875B MET* 3.7 20.0 - - + +
880B LEU* 3.8 25.8 - - + -
888B LEU* 4.9 0.6 - - + +
1128B GLY 3.2 8.2 + - - +
1129B SER* 3.1 12.0 + - - +
1131B ALA* 1.3 78.0 - - - +
1133B ILE* 1.3 58.1 + - - +
1135B GLU* 3.1 18.4 + - - +
1136B GLY 3.1 6.6 + - - -
1137B CYS* 3.0 29.7 + - + +
1143B CYS* 5.0 0.9 - - - -
1152B VAL* 3.9 6.8 - - + +
1153B ALA* 4.8 1.3 - - + -
3508B FMN 3.7 38.4 - - + -
3509B F3S 3.5 33.4 - - - -
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Residues in contact with ILE1133 (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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797B ASN* 3.6 28.3 - - - +
801B MET* 3.8 7.9 - - + -
802B SER* 3.4 50.0 - - - +
805B LEU* 3.8 16.6 - - + -
806B HIS* 3.6 8.8 + - - +
1129B SER 2.9 19.6 + - - +
1130B ILE* 3.5 15.7 - - + +
1131B ALA 3.2 0.2 - - - -
1132B MET* 1.3 72.2 - - - +
1134B ALA* 1.3 58.4 + - - +
1135B GLU 3.0 4.5 - - - -
1136B GLY* 2.9 20.1 + - - -
1137B CYS* 3.7 23.4 + - - +
1139B MET* 4.2 7.4 - - + -
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Residues in contact with ALA1134 (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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805B LEU* 4.7 6.5 - - + +
806B HIS* 3.1 11.9 + - - +
809B VAL* 3.6 13.9 - - + +
1130B ILE 3.0 14.2 + - - +
1131B ALA* 3.5 11.0 - - - +
1133B ILE* 1.3 77.1 - - - +
1135B GLU* 1.3 56.4 + - - +
1136B GLY 3.4 0.2 - - - -
1169B GLN* 3.1 19.8 - - - +
1170B VAL* 4.3 14.6 - - + -
1173B PHE* 4.0 33.9 - - + -
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Residues in contact with GLU1135 (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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806B HIS* 3.8 4.5 - - - -
880B LEU* 5.4 0.2 - - - +
884B ALA* 2.5 41.7 - - - +
887B THR* 3.1 24.5 - - + +
888B LEU* 3.4 25.4 + - + +
1131B ALA 3.2 10.0 + - - +
1132B MET* 3.2 20.4 - - - +
1133B ILE 3.0 0.2 - - - -
1134B ALA* 1.3 77.1 - - - +
1136B GLY* 1.3 55.2 + - - +
1137B CYS 3.8 0.2 - - - -
1152B VAL* 4.9 3.3 - - + +
1163B PHE* 3.4 23.6 - - + -
1164B LYS 3.1 22.3 - - - +
1165B GLY* 4.1 2.0 - - - -
1169B GLN* 4.0 5.6 - - - -
1170B VAL* 3.8 12.3 - - + -
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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
------------------------------------------------------------
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