Contacts of the helix formed by residues 250 - 255 (chain A) in PDB entry 1QCO
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A GLU* 2.9 21.1 + - + +
248A GLY 3.5 3.8 + - - +
249A PRO* 1.3 75.0 - - - +
251A LEU* 1.3 91.3 + - + +
252A GLY 4.2 0.8 - - - +
253A LYS* 3.2 4.4 + - - +
254A SER* 3.2 24.0 + - - -
625B THR* 3.6 30.3 - - + -
627B PHE* 4.4 16.2 - + - -
656B PRO 5.3 0.2 - - - -
657B VAL* 6.0 0.2 - - - -
658B GLY* 3.6 30.5 - - - +
659B TYR* 4.0 10.3 - - - -
660B HIS* 3.5 37.2 + + - -
832B HIS* 4.4 12.3 - + - -
833B HIS* 3.9 20.4 - + - -
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Residues in contact with LEU 251 (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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178A GLY* 5.9 2.2 - - - -
179A GLN 6.2 0.4 - - - +
236A ALA* 5.0 0.9 - - - +
239A ILE* 4.2 14.6 - - + +
243A GLU* 2.9 11.1 + - - +
250A PHE* 1.3 98.4 - - + +
252A GLY* 1.3 57.6 + - - +
253A LYS 3.0 10.1 + - - -
254A SER* 3.5 6.1 - - - +
255A PHE* 3.6 8.0 - - - -
832B HIS* 3.3 47.1 - - + +
833B HIS* 3.7 26.5 - - - +
835B VAL* 3.7 14.4 - - + -
836B ASN* 2.8 40.3 + - + +
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Residues in contact with GLY 252 (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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235A SER* 3.3 8.1 - - - -
236A ALA* 2.9 44.8 + - - +
239A ILE* 4.0 8.9 - - - +
240A GLN* 4.2 8.3 - - - +
243A GLU* 2.8 17.2 + - - -
250A PHE 3.2 0.2 - - - -
251A LEU* 1.3 76.7 - - - +
253A LYS* 1.3 64.1 + - - +
255A PHE* 3.5 3.4 - - - -
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Residues in contact with LYS 253 (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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159A TYR* 3.7 13.7 - - + +
199A GLU* 2.8 30.5 + - - -
233A ASP* 3.5 17.6 + - - +
234A TRP 3.8 5.8 - - - +
235A SER* 2.8 29.8 + - - +
237A ARG* 4.0 3.6 - - - +
240A GLN* 3.7 17.9 - - - +
249A PRO* 3.7 23.6 - - + -
250A PHE 3.2 6.0 + - - +
251A LEU 3.0 0.4 - - - -
252A GLY* 1.3 84.3 - - - +
254A SER* 1.3 63.3 + - - +
255A PHE* 3.3 6.9 + - - -
256A GLY 3.5 17.7 + - - +
257A THR* 3.8 8.7 + - - -
1008A FUM 5.1 0.2 + - - -
1010A AAE 3.2 23.3 + - - +
660B HIS* 5.4 3.1 - - - +
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Residues in contact with SER 254 (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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162A ARG* 3.6 28.7 - - - -
165A SER* 2.6 29.1 + - - -
250A PHE 3.2 14.3 + - - -
251A LEU* 3.5 10.1 + - - +
253A LYS* 1.3 75.9 - - - +
255A PHE* 1.3 58.7 + - - +
256A GLY 3.1 3.1 - - - -
257A THR* 5.6 0.4 - - - -
660B HIS* 4.0 8.5 - - - -
833B HIS* 5.3 0.7 - - - -
836B ASN* 3.0 17.8 + - - -
838B CYS* 3.8 15.9 - - - +
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Residues in contact with PHE 255 (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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173A ILE* 3.8 20.9 - - + +
174A ARG 4.1 3.6 - - - +
176A PRO* 3.9 23.8 - - + -
196A LEU* 3.5 31.0 - - + -
234A TRP* 3.7 37.2 - - + -
235A SER 3.8 0.9 - - - -
236A ALA* 3.6 12.8 - - + -
251A LEU 3.6 14.4 - - - -
252A GLY 3.5 22.2 - - - -
253A LYS 4.2 0.9 - - - -
254A SER* 1.3 77.3 - - - +
256A GLY* 1.3 57.0 + - - +
712B PHE* 3.2 23.5 - - - -
713B GLY* 5.7 0.9 + - - -
836B ASN* 3.3 36.4 - - - +
837B GLY 5.1 2.3 - - - +
838B CYS* 4.6 4.5 - - - +
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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