Contacts of the helix formed by residues 250 - 255 (chain B) in PDB entry 1QQJ
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 PHE 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A THR* 3.7 30.1 - - + -
127A PHE* 4.4 16.2 - + - -
156A PRO 5.4 0.2 - - - -
157A VAL* 6.1 0.4 - - - -
158A GLY* 3.6 28.3 - - - +
159A TYR* 3.9 9.9 - - - -
160A HIS* 3.5 35.1 - + - -
332A HIS* 4.5 11.4 - + - -
333A HIS* 3.7 21.1 - + - -
243B GLU* 2.9 19.8 + - + +
248B GLY 3.9 3.4 - - - +
249B PRO* 1.3 74.7 - - - +
251B LEU* 1.3 87.3 + - + +
252B GLY 3.1 1.0 - - - +
253B LYS* 3.0 20.3 + - - +
254B SER* 3.1 17.2 + - - -
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Residues in contact with LEU 251 (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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332A HIS* 3.2 49.8 - - + +
333A HIS* 3.7 26.5 - - + +
335A VAL* 3.7 13.5 - - + -
336A ASN* 2.9 39.5 + - + +
178B GLY* 6.0 1.6 - - - -
179B GLN 6.2 0.4 - - - +
236B ALA* 4.9 1.0 - - - +
239B ILE* 4.0 15.3 - - + +
243B GLU* 2.9 10.9 + - - +
250B PHE* 1.3 100.9 - - + +
252B GLY* 1.3 60.1 + - - +
253B LYS 3.1 1.9 + - - -
254B SER* 3.6 5.8 - - - +
255B PHE* 3.6 8.5 - - - -
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Residues in contact with GLY 252 (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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235B SER* 3.3 8.1 - - - -
236B ALA* 2.8 45.6 + - - -
239B ILE* 3.8 7.1 - - - +
240B GLN* 4.0 9.1 - - - +
243B GLU* 2.8 17.7 + - - -
251B LEU* 1.3 76.3 - - - +
253B LYS* 1.3 62.7 + - - +
255B PHE* 3.4 3.3 - - - -
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Residues in contact with LYS 253 (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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160A HIS* 5.1 4.0 - - + -
124B TYR* 6.6 0.4 - - + -
159B TYR* 3.5 23.6 - - + +
199B GLU* 2.9 20.0 + - - -
233B ASP* 3.3 22.0 + - - +
234B TRP 3.8 5.3 - - - +
235B SER* 2.8 24.7 + - - +
240B GLN* 3.6 17.3 - - - +
249B PRO* 3.6 21.3 - - + -
250B PHE 3.0 6.6 + - - +
252B GLY* 1.3 82.8 - - - +
254B SER* 1.3 59.2 + - - +
255B PHE* 3.2 9.6 + - - -
256B GLY 3.5 18.5 + - - +
257B THR* 3.8 8.9 + - - +
420B CA 3.7 2.4 - - - -
2003B CAC 3.0 28.1 + - - -
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Residues in contact with SER 254 (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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160A HIS* 3.8 9.1 + - - -
333A HIS* 5.2 1.0 - - - -
336A ASN* 3.0 16.6 + - - -
338A CYS* 3.7 17.6 - - - +
162B ARG* 3.6 28.7 - - - -
165B SER* 2.7 28.7 + - - -
250B PHE 3.1 14.5 + - - -
251B LEU* 3.6 11.3 + - - +
253B LYS* 1.3 74.0 - - - +
255B PHE* 1.3 59.4 + - - +
256B GLY 3.2 2.5 - - - -
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Residues in contact with PHE 255 (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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212A PHE* 3.1 23.2 - - - -
213A GLY* 5.7 1.0 + - - -
336A ASN* 3.1 36.9 - - - +
337A GLY 5.0 2.4 - - - +
338A CYS 4.4 4.7 - - - +
173B ILE* 3.8 20.9 - - + +
174B ARG 4.0 3.7 + - - +
176B PRO* 3.8 26.5 - - + -
196B LEU* 3.6 24.7 - - + -
234B TRP* 3.7 37.0 - - + -
235B SER 3.8 0.9 - - - -
236B ALA* 3.5 11.9 - - + -
251B LEU 3.6 14.1 - - - -
252B GLY 3.4 22.2 - - - -
253B LYS 4.2 1.8 - - - -
254B SER* 1.3 78.3 - - - +
256B GLY* 1.3 57.4 + - - +
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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