Contacts of the helix formed by residues 183 - 188 (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 ILE 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ASP 5.8 0.4 - - - +
116B VAL* 3.7 40.4 - - + +
117B LEU* 4.9 1.6 - - + -
179B VAL* 3.8 23.8 - - + -
180B ARG* 2.9 43.5 + - + +
182B ILE* 1.3 100.4 - - + +
184B LEU* 1.3 65.3 + - - +
185B GLY 3.3 0.9 - - - -
186B GLU* 2.9 11.3 + - + -
187B PHE* 2.9 21.4 + - + +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.1 9.4 - - + -
25B LEU* 3.9 18.2 - - + -
44B ALA* 3.4 22.2 - - + +
45B GLY* 3.7 24.9 - - - +
46B VAL* 4.1 2.9 - - + +
175B TYR 3.9 9.0 - - - +
176B LYS* 4.1 1.6 - - - -
177B GLY* 4.1 1.6 - - - +
179B VAL* 3.7 19.0 - - + +
180B ARG 3.4 3.4 + - - -
181B SER 3.3 14.5 + - - +
183B ILE* 1.3 76.1 - - - +
185B GLY* 1.3 58.4 + - - +
187B PHE* 3.4 3.1 + - + +
188B TYR* 3.0 57.6 + - + +
191B LEU* 4.0 15.7 - - + -
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.2 9.5 - - - +
181B SER 4.7 1.0 + - - -
182B ILE 4.6 2.8 + - - -
183B ILE 3.3 0.2 - - - -
184B LEU* 1.3 76.4 - - - +
186B GLU* 1.3 61.3 + - - +
187B PHE 3.4 0.2 - - - -
188B TYR 3.3 10.5 - - - +
189B LEU* 4.8 1.7 - - - +
191B LEU* 4.1 19.5 - - - -
192B LYS* 3.1 42.3 - - - +
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Residues in contact with GLU 186 (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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113B ASN* 3.7 17.7 + - - +
116B VAL* 3.9 23.8 - - + +
182B ILE 3.5 19.9 + - - +
183B ILE* 2.9 15.6 + - + +
185B GLY* 1.3 75.7 - - - +
187B PHE* 1.3 63.0 + - - +
189B LEU* 3.7 9.4 - - - +
192B LYS* 3.2 28.1 + - - +
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Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 3.0 26.3 - - + +
113B ASN 2.9 39.2 + - - -
114B SER* 4.0 5.4 - - - -
116B VAL* 3.7 11.2 - - + +
117B LEU* 3.6 35.0 - - + -
125B GLN* 3.7 28.9 - - - -
128B ILE* 3.7 23.3 - - + -
177B GLY* 6.0 0.2 - - - -
179B VAL* 4.8 5.4 - - + -
183B ILE* 2.9 16.4 + - + +
184B LEU* 3.8 3.1 - - + +
186B GLU* 1.3 79.0 - - - +
188B TYR* 1.3 88.2 + + - +
189B LEU* 3.4 1.9 + - - +
215B TRP* 3.9 17.5 - + - -
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Residues in contact with TYR 188 (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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76B MET* 3.9 21.1 - - + +
78B PHE* 3.8 8.8 - - - -
110B VAL* 3.9 10.8 - - + -
111B PRO 4.0 1.1 - - - -
112B VAL* 3.9 12.1 - - + -
128B ILE* 3.6 21.3 - - + +
175B TYR* 3.5 22.4 - + + -
176B LYS 2.7 47.8 + - - -
177B GLY* 5.0 0.2 - - - -
184B LEU* 3.0 34.6 + - + +
185B GLY 3.3 14.5 - - - +
187B PHE* 1.3 97.6 - + - +
189B LEU* 1.3 65.5 + - - +
190B ASP 3.1 1.6 - - - +
191B LEU* 3.0 27.1 + - + +
215B TRP* 4.3 0.2 - - - -
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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