Contacts of the helix formed by residues 291 - 300 (chain B) in PDB entry 5H65
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 291 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574A LEU 3.8 5.1 + - - +
575A MET* 4.4 7.6 - - - +
576A ASP 4.3 6.3 - - - +
577A ASP* 3.6 35.0 - - + +
580A GLN* 2.9 30.1 + - - +
290B VAL* 1.3 81.0 - - - +
292B HIS* 1.3 60.6 + - - +
294B ALA* 3.2 16.6 + - - +
295B ALA* 3.0 22.9 + - - +
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Residues in contact with HIS 292 (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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577A ASP* 2.8 29.7 + - - +
580A GLN* 3.5 26.8 + - + -
581A LYS* 3.7 27.7 + - + +
584A ASP* 2.7 28.4 + - - -
291B THR* 1.3 71.9 - - - +
293B TRP* 1.3 71.4 + + - +
295B ALA* 3.6 9.1 - - - +
296B SER* 2.9 29.2 + - - -
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Residues in contact with TRP 293 (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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374A LEU* 3.8 21.5 - - + +
375A PHE* 3.6 37.7 - + + -
377A SER* 4.7 0.2 - - - -
378A VAL* 4.0 16.2 - - + -
542A PHE* 4.6 4.9 - + - -
573A VAL* 3.7 20.2 - - + -
574A LEU* 4.0 14.1 - - + -
580A GLN* 3.1 41.6 + - + +
583A VAL* 3.8 32.1 - - + -
584A ASP* 3.0 31.6 + - - -
292B HIS* 1.3 94.2 + + - +
294B ALA* 1.3 53.7 + - - +
296B SER* 3.2 8.2 + - - -
297B ARG* 2.7 36.3 + - - +
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Residues in contact with ALA 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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394A GLU* 6.2 3.1 - - + -
574A LEU 5.2 5.4 + - - +
580A GLN* 4.9 0.2 - - - +
290B VAL* 3.4 31.1 - - + +
291B THR* 3.2 14.8 + - - +
293B TRP* 1.3 78.3 - - - +
295B ALA* 1.3 57.7 + - - +
297B ARG* 3.4 12.8 - - - +
298B CYS* 3.0 27.5 + - - +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 4.0 15.4 - - + +
291B THR 3.0 13.4 + - - +
292B HIS* 3.6 13.5 - - + +
294B ALA* 1.3 73.9 - - - +
296B SER* 1.3 64.6 + - - +
298B CYS* 3.4 6.4 + - - +
299B LYS* 3.1 27.8 + - - +
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Residues in contact with SER 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ARG* 5.0 5.0 - - - +
375A PHE* 3.6 17.0 - - - -
292B HIS* 2.9 18.0 + - - -
293B TRP* 3.5 9.0 - - - -
295B ALA* 1.3 75.7 - - - +
297B ARG* 1.3 57.5 + - - +
299B LYS* 3.6 6.3 + - - +
300B ALA* 3.0 30.8 + - - +
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Residues in contact with ARG 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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375A PHE* 3.6 45.4 + - + -
376A GLN* 6.0 1.2 - - - +
378A VAL 5.2 3.0 + - - -
390A GLU* 4.8 7.9 + - - -
391A VAL* 3.2 34.5 + - - +
392A PRO 4.4 6.9 + - - -
393A HIS* 3.0 47.9 + - + +
394A GLU 5.9 0.2 - - - +
574A LEU* 4.0 32.1 - - - +
293B TRP 2.7 19.8 + - - +
294B ALA* 3.4 15.0 - - - +
296B SER* 1.3 71.5 - - - +
298B CYS* 1.3 64.2 + - - +
300B ALA* 3.4 9.2 + - - +
301B THR* 3.3 14.9 + - - -
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Residues in contact with CYS 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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394A GLU* 5.6 5.8 - - - -
294B ALA 3.0 17.2 + - - +
295B ALA* 3.4 7.6 + - - +
297B ARG* 1.3 76.9 - - - +
299B LYS* 1.3 60.9 + - + +
301B THR* 2.8 24.3 + - - -
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Residues in contact with LYS 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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295B ALA 3.1 20.1 + - - +
296B SER* 3.8 7.2 - - - +
297B ARG 3.3 0.2 - - - -
298B CYS* 1.3 77.5 - - + +
300B ALA* 1.3 56.8 + - + +
301B THR* 3.2 9.4 + - - +
303B GLU* 4.2 2.6 - - - +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ARG* 3.7 33.2 - - - +
375A PHE* 4.2 13.2 - - + -
376A GLN* 5.5 3.1 + - - +
296B SER* 3.0 19.5 + - - +
297B ARG 3.4 4.7 + - - +
298B CYS 3.4 0.6 - - - -
299B LYS* 1.3 72.9 - - - +
301B THR* 1.3 60.3 + - - +
302B GLY 3.5 0.2 + - - -
303B GLU* 2.9 32.0 + - - +
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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