Contacts of the helix formed by residues 293 - 299 (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 VAL 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A ARG* 5.8 0.5 - - - -
270B ALA 5.3 2.7 - - - +
271B PHE 3.7 9.6 - - - +
272B ALA 3.4 9.9 - - - +
273B GLY* 3.8 20.4 - - - -
287B LEU 3.8 12.8 - - - +
288B ALA 3.1 20.4 - - - +
289B GLN 3.9 2.5 - - - +
290B ARG 3.8 0.2 + - - -
291B PRO 3.4 3.0 - - - -
292B GLY* 1.3 87.1 - - - +
294B ARG* 1.3 56.4 + - - +
295B GLN* 2.5 22.0 + - - +
296B GLY* 2.8 15.6 + - - -
297B TRP* 3.2 29.3 + - + +
532B GLN* 6.0 1.6 - - + -
535B GLY* 4.0 14.1 - - - +
536B GLY 4.5 0.4 - - - +
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Residues in contact with ARG 294 (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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288B ALA 3.3 7.4 + - - +
289B GLN* 4.0 32.8 - - - +
290B ARG 3.8 10.0 + - - +
293B VAL* 1.3 74.5 - - - +
295B GLN* 1.3 59.4 + - - +
297B TRP* 3.0 9.8 + - - +
298B LEU* 2.2 44.4 + - + +
326B VAL* 4.5 9.3 - - + +
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Residues in contact with GLN 295 (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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525A HIS* 5.3 3.6 - - - +
526A ALA 3.3 11.7 + - - -
527A ASP* 2.7 53.5 + - + +
528A ARG* 5.0 5.6 - - + +
290B ARG 4.5 9.3 + - - -
291B PRO* 4.8 1.0 - - - +
292B GLY 5.9 0.9 - - - +
293B VAL 2.5 11.5 + - - +
294B ARG* 1.3 76.2 - - - +
296B GLY* 1.3 57.4 + - - +
298B LEU* 2.8 9.3 + - - +
299B ASN* 2.3 55.9 + - - +
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Residues in contact with GLY 296 (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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251B VAL* 4.5 2.1 - - - +
271B PHE* 3.6 18.3 - - - -
293B VAL 2.8 12.2 + - - -
295B GLN* 1.3 72.7 - - - +
297B TRP* 1.3 55.8 + - - -
299B ASN* 3.0 11.8 - - - +
300B CYS* 2.8 26.9 - - - -
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Residues in contact with TRP 297 (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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271B PHE* 3.8 25.3 + + - -
272B ALA* 2.5 49.9 + - + +
288B ALA* 4.3 8.0 - - + +
293B VAL* 3.2 22.3 + - + +
294B ARG* 3.0 16.1 + - - +
296B GLY* 1.3 76.2 - - - +
298B LEU* 1.3 63.2 + - - +
300B CYS* 3.5 12.9 - - - +
319B LEU* 3.8 16.6 - - + -
322B VAL* 4.3 16.2 - - + -
323B ALA* 3.3 42.4 - - + -
326B VAL* 4.8 16.2 - - + -
327B ARG* 5.4 7.5 - - + +
333B PHE* 3.9 20.4 - + - -
336B ILE* 4.8 8.0 - - + +
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Residues in contact with LEU 298 (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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294B ARG* 2.2 35.0 + - + +
295B GLN* 2.8 10.4 + - - +
297B TRP* 1.3 72.4 - - - +
299B ASN* 1.3 65.4 + - - +
300B CYS 3.1 11.1 + - - +
326B VAL* 6.3 2.7 - - + -
327B ARG* 5.6 9.9 - - + +
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Residues in contact with ASN 299 (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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487A LEU* 5.6 7.5 - - - +
248B THR 4.7 5.8 - - - +
251B VAL* 4.8 2.1 - - - +
295B GLN* 2.3 42.0 + - - +
296B GLY* 3.0 14.0 - - - +
298B LEU* 1.3 71.5 - - - +
300B CYS* 1.3 64.6 + - - +
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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