Contacts of the helix formed by residues 256 - 264 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ALA* 2.8 17.7 - - - +
255B SER* 1.3 83.2 + - - +
257B GLY* 1.3 75.5 + - - +
258B VAL* 3.6 25.4 - - + +
259B ALA* 3.9 12.5 + - - -
260B ALA* 3.8 9.2 + - - +
267B THR* 4.0 2.1 + - - -
307B GLU* 4.3 3.8 - - - +
310B MET* 3.0 31.5 - - - +
555B HIS* 4.3 31.5 + - + +
556B LYS* 4.9 2.5 - - - -
558B GLN 5.6 2.6 + - - +
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Residues in contact with GLY 257 (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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255B SER 4.0 0.6 + - - -
256B THR* 1.3 77.7 - - - +
258B VAL* 1.3 63.6 + - - +
260B ALA* 3.3 19.2 - - - +
261B CYS* 4.0 2.4 + - - +
267B THR* 4.3 4.8 + - - -
466B GLN* 3.3 38.2 - - - +
468B PRO* 4.7 8.3 - - - +
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 3.6 15.0 - - + +
257B GLY* 1.3 71.0 - - - +
259B ALA* 1.3 71.3 + - - +
260B ALA 3.0 4.0 + - - -
261B CYS* 3.0 18.3 + - + +
262B HIS* 3.3 9.0 + - + +
468B PRO* 4.5 19.1 - - + +
484B VAL* 5.0 14.8 - - + -
493B LEU* 5.1 7.1 - - + +
556B LYS* 3.2 30.3 - - + +
558B GLN 4.7 8.3 - - - +
560B MET* 4.8 16.8 - - - -
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Residues in contact with ALA 259 (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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254B ALA* 3.6 19.6 - - + +
256B THR* 3.9 14.9 + - - +
257B GLY 3.4 0.6 - - - -
258B VAL* 1.3 83.6 - - + +
260B ALA* 1.3 62.8 + - - +
262B HIS* 3.5 14.6 - - + +
263B ILE* 3.2 25.3 + - + +
306B ASP* 5.2 3.8 - - + +
307B GLU* 4.6 15.3 - - + +
558B GLN 5.4 5.4 - - - +
559B GLY* 6.1 1.6 - - - -
701B ADP 6.0 1.8 - - - +
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Residues in contact with ALA 260 (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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254B ALA* 3.7 7.9 - - - +
256B THR 3.8 4.4 + - - +
257B GLY 3.3 14.5 + - - +
258B VAL 3.0 0.2 - - - -
259B ALA* 1.3 77.5 - - - +
261B CYS* 1.3 49.9 + - - +
263B ILE* 2.8 6.1 + - - -
264B GLY 2.3 34.0 + - - -
265B GLY* 2.9 22.3 + - - +
266B THR* 3.1 31.9 - - - +
267B THR* 4.4 1.3 - - - +
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Residues in contact with CYS 261 (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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257B GLY 4.0 2.4 + - - +
258B VAL* 3.0 11.1 + - + +
260B ALA* 1.3 75.0 - - - +
262B HIS* 1.3 67.0 + - - +
264B GLY* 3.2 14.1 + - - +
265B GLY 5.1 0.2 - - - -
468B PRO* 6.5 1.1 - - + -
485B LYS* 3.4 43.1 - - + -
486B ASN 4.7 2.0 - - - -
493B LEU* 5.2 6.4 - - + +
529B TRP* 5.4 8.1 - - + +
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Residues in contact with HIS 262 (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* 4.3 28.0 + - - -
236B TYR* 5.6 2.3 - + - -
239B LYS* 5.7 4.3 - - - +
258B VAL* 3.3 7.3 + - + +
259B ALA* 3.5 17.3 - - + +
261B CYS* 1.3 79.5 - - - +
263B ILE* 1.3 65.8 + - + +
493B LEU* 4.7 27.4 - - + +
559B GLY 4.8 10.5 - - - -
701B ADP 3.9 32.0 - + - -
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Residues in contact with ILE 263 (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* 5.2 7.2 - - - +
238B LEU* 3.9 21.5 - - + -
239B LYS* 5.4 8.7 - - + +
242B LEU* 3.3 37.9 - - + +
252B ALA* 3.9 18.2 - - + -
253B THR 4.7 9.6 - - - +
254B ALA* 5.2 0.2 - - + -
259B ALA* 3.2 11.6 + - + +
260B ALA* 2.8 7.1 + - - +
261B CYS 4.0 0.2 - - - -
262B HIS* 1.3 88.5 - - + +
264B GLY* 1.3 57.6 + - - +
265B GLY* 4.0 5.2 - - - +
304B VAL* 5.1 2.0 - - + -
306B ASP* 3.7 31.9 - - + +
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Residues in contact with GLY 264 (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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242B LEU* 5.8 0.7 - - - -
260B ALA 2.3 19.6 + - - -
261B CYS* 3.2 15.0 + - - -
263B ILE* 1.3 69.7 - - - +
265B GLY* 1.3 63.3 + - - +
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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