Contacts of the helix formed by residues 256 - 264 (chain A) in PDB entry 5FHH
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 THR 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ALA* 4.2 1.0 - - - +
255A SER* 1.3 82.2 - - - +
257A GLY* 1.3 64.3 + - - +
258A VAL* 3.2 15.7 - - + +
259A ALA* 2.8 32.5 + - - +
260A ALA* 3.4 14.2 + - - +
267A THR* 3.7 16.8 - - - +
310A MET* 3.6 26.4 - - + +
555A HIS* 4.0 32.1 - - + +
558A GLN* 5.5 1.0 + - + -
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 1.3 72.6 - - - +
258A VAL* 1.3 62.1 + - - +
260A ALA* 3.3 12.0 + - - +
261A CYS* 3.2 16.3 + - - +
267A THR* 4.1 13.5 - - - +
466A GLN 4.5 4.5 - - - +
467A CYS* 4.3 23.5 - - - -
468A PRO* 4.2 8.5 - - - +
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Residues in contact with VAL 258 (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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256A THR* 3.2 19.7 - - + +
257A GLY* 1.3 72.5 - - - +
259A ALA* 1.3 58.4 + - - +
260A ALA 3.4 0.2 - - - -
261A CYS* 3.2 20.2 - - - -
262A HIS* 3.6 11.6 + - - +
468A PRO* 4.2 20.1 - - + +
493A LEU* 5.4 6.9 - - + +
555A HIS 5.4 0.2 - - - +
556A LYS* 3.6 34.8 - - + +
558A GLN 4.4 11.2 - - - +
559A GLY* 5.4 3.0 - - - +
560A MET* 4.1 20.9 - - + -
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Residues in contact with ALA 259 (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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254A ALA* 3.4 20.3 - - + +
255A SER 4.2 2.2 - - - +
256A THR* 2.8 27.9 + - - +
258A VAL* 1.3 71.4 - - - +
260A ALA* 1.3 64.3 + - - +
262A HIS* 3.5 5.7 + - - +
263A ILE* 3.4 27.2 + - - +
306A ASP* 5.1 6.5 - - + +
307A GLU* 4.5 15.0 - - + -
558A GLN 5.7 3.4 - - - +
559A GLY* 5.8 6.5 - - - -
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Residues in contact with ALA 260 (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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252A ALA 4.9 0.4 - - - -
254A ALA* 3.5 7.6 - - + +
256A THR 3.4 4.4 + - - +
257A GLY 3.3 5.1 + - - +
259A ALA* 1.3 78.5 - - - +
261A CYS* 1.3 60.7 + - - +
263A ILE* 3.2 2.3 + - - +
264A GLY 3.0 28.2 + - - +
265A GLY* 3.2 22.5 + - - +
266A THR 3.3 26.9 - - - +
267A THR* 3.8 18.4 - - + -
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Residues in contact with CYS 261 (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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257A GLY 3.2 14.2 + - - +
258A VAL* 3.2 29.2 - - - -
260A ALA* 1.3 76.8 - - - +
262A HIS* 1.3 64.9 + - - +
263A ILE 3.4 3.3 + - - +
264A GLY 5.2 3.6 - - - +
265A GLY* 5.6 0.4 - - - -
468A PRO* 4.0 21.1 - - + -
484A VAL 5.3 6.3 - - - +
485A LYS* 5.1 19.9 - - + +
486A ASN* 5.4 4.7 - - - +
493A LEU* 5.5 8.1 - - - -
529A TRP* 5.5 7.4 - - + +
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Residues in contact with HIS 262 (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* 5.2 16.3 + - - -
239A LYS* 6.0 2.3 - - - +
258A VAL 3.6 11.9 + - - +
259A ALA* 3.5 12.1 + - - +
260A ALA 3.2 0.6 - - - -
261A CYS* 1.3 80.9 - - - +
263A ILE* 1.3 63.5 - - + +
493A LEU* 4.6 29.2 - - + +
559A GLY* 3.1 28.4 + - - -
560A MET* 5.6 0.9 - - - -
561A THR* 5.9 3.4 - - - -
701A ADP 5.2 19.3 - - - -
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Residues in contact with ILE 263 (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* 5.1 9.2 - - - +
238A LEU* 4.1 23.3 - - + +
239A LYS* 5.6 2.5 - - - +
242A LEU* 3.5 31.6 - - + +
252A ALA* 4.5 10.3 - - + +
253A THR 4.1 7.9 - - - +
259A ALA 3.4 15.3 - - - +
260A ALA* 3.2 3.6 + - - +
261A CYS 3.2 2.8 - - - +
262A HIS* 1.3 85.8 - - + +
264A GLY* 1.3 60.8 + - - +
304A VAL* 4.8 4.5 - - + -
306A ASP* 3.1 43.3 - - + +
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Residues in contact with GLY 264 (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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242A LEU* 4.7 2.7 - - - -
252A ALA* 3.8 15.7 - - - +
260A ALA 3.0 8.9 + - - +
261A CYS* 5.2 3.2 - - - +
263A ILE* 1.3 83.7 - - - +
265A GLY* 1.3 57.2 + - - +
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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
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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