Contacts of the strand formed by residues 235 - 240 (chain A) in PDB entry 1QFM
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 MET 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE* 3.5 34.8 - - + +
190A TYR* 3.4 23.6 - - - +
208A GLN* 3.4 25.4 - - + +
228A PHE* 4.7 0.2 - - - -
233A LYS 3.6 11.2 - - - +
234A TRP* 1.3 80.5 - - - +
236A GLY* 1.3 58.9 + - - +
237A GLY 3.9 1.0 + - - -
250A SER 3.4 2.8 - - - +
251A ILE* 3.3 3.7 - - - -
252A ARG* 2.8 48.4 + - + +
254A GLY 6.1 2.2 - - - -
591A ILE* 4.2 8.5 - - - -
593A HIS* 5.1 2.9 - - - -
782A SGL 3.9 26.2 - - - -
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Residues in contact with GLY 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ASN* 2.8 26.8 + - - +
208A GLN* 3.8 6.0 + - - -
209A LYS 6.3 0.4 - - - -
210A LEU* 4.0 6.1 - - - +
228A PHE* 3.7 22.4 - - - -
235A MET* 1.3 70.5 - - - +
237A GLY* 1.3 61.0 + - - -
238A ALA 3.9 0.9 + - - -
249A LEU* 3.5 19.7 - - - +
250A SER 3.5 4.9 - - - -
251A ILE* 4.2 3.4 - - - -
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A CSD 3.5 28.3 - - - -
188A ASN* 4.2 4.3 - - - -
235A MET 3.9 1.6 + - - -
236A GLY* 1.3 72.4 - - - -
238A ALA* 1.3 60.3 + - - -
239A GLU* 5.8 0.2 - - - +
248A LEU 3.5 2.1 - - - +
249A LEU* 3.4 3.6 - - - -
250A SER* 2.8 41.1 + - - +
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A CSD 3.8 20.0 - - - +
177A ALA* 3.6 13.5 - - - +
186A PHE* 4.1 14.7 - - + +
188A ASN* 5.1 0.2 + - - -
210A LEU* 3.7 30.4 - - + +
236A GLY 3.9 2.0 + - - -
237A GLY* 1.3 73.4 - - - -
239A GLU* 1.3 63.0 + - - +
247A VAL* 3.9 21.3 - - + -
248A LEU 3.3 5.2 - - - +
249A LEU* 4.3 2.2 - - + -
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ALA* 3.8 9.4 - - + -
237A GLY 5.8 0.4 - - - +
238A ALA* 1.3 76.4 - - - +
240A LEU* 1.3 69.2 + - - +
247A VAL* 3.4 4.3 - - - +
248A LEU* 2.8 51.4 + - + +
250A SER* 4.4 12.3 + - - -
261A LEU* 5.7 0.7 - - - +
292A TYR* 3.5 42.6 + - - +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ALA* 4.1 9.8 - - + +
178A TRP 3.4 29.8 - - - +
179A THR* 4.0 9.2 - - + -
180A HIS* 3.8 21.2 + - + +
186A PHE* 4.0 23.8 - - + -
239A GLU* 1.3 86.5 - - - +
241A SER* 1.3 65.1 + - - +
242A ASP* 3.8 1.7 + - - +
244A GLY 3.9 11.4 - - - +
246A TYR 3.4 13.7 - - - +
247A VAL* 4.0 7.0 - - + -
266A LEU* 3.8 28.0 - - + -
292A TYR* 4.3 6.4 - - - -
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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