Contacts of the helix formed by residues 607 - 613 (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 VAL 607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A PHE* 4.2 24.7 - - + +
345A LEU* 3.9 22.9 - - + -
359A PHE* 4.1 16.6 - - + -
361A PHE* 3.3 38.8 - - + -
605A PRO* 3.2 26.9 + - + +
606A ARG* 1.3 72.6 - - - +
608A LEU* 1.3 54.3 + - - +
609A HIS 2.9 5.6 - - - -
610A PHE* 2.7 29.4 + - + +
611A TYR* 3.4 7.7 + - + -
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Residues in contact with LEU 608 (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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345A LEU* 4.8 11.2 - - + -
396A LEU* 5.3 20.0 - - + +
604A ASP* 5.8 3.8 - - + +
605A PRO* 5.3 1.1 - - + +
606A ARG* 3.9 7.8 - - - +
607A VAL* 1.3 83.2 - - - +
609A HIS* 1.3 49.9 + - - +
611A TYR* 3.2 11.9 + - - +
612A ALA* 2.6 37.4 + - + +
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Residues in contact with HIS 609 (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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606A ARG* 3.1 18.9 + - + +
607A VAL* 2.9 0.4 - - - -
608A LEU* 1.3 77.2 - - - +
610A PHE* 1.3 58.5 + - - +
612A ALA* 2.9 8.7 + - + +
613A THR* 2.8 51.5 + - + +
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Residues in contact with PHE 610 (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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225A PHE* 4.3 26.2 - + - -
344A PHE* 5.4 2.7 - + - -
361A PHE* 3.7 61.5 - + + -
366A TRP* 5.6 4.7 - + - -
373A THR* 5.0 5.4 - - + -
607A VAL 2.7 15.9 + - - +
609A HIS* 1.3 76.4 + - - +
611A TYR* 1.3 88.1 + + - +
613A THR* 3.2 23.4 + - - -
614A LEU* 3.3 37.9 - - + +
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Residues in contact with TYR 611 (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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225A PHE* 4.8 0.2 - - - -
227A THR* 2.3 52.8 + - + -
343A ASP* 3.5 1.8 - - - -
344A PHE* 3.1 45.5 + + + -
345A LEU* 4.3 27.8 - - + -
395A ARG* 4.5 14.8 - - - -
607A VAL* 3.4 10.3 + - + -
608A LEU* 3.2 11.7 + - - +
610A PHE* 1.3 97.6 - + - +
612A ALA* 1.3 59.4 + - - +
614A LEU* 3.4 28.3 - - + +
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Residues in contact with ALA 612 (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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608A LEU* 2.6 21.2 + - + +
609A HIS* 2.9 12.9 + - - +
611A TYR* 1.3 72.1 - - - +
613A THR* 1.3 62.1 + - + +
614A LEU 3.0 7.2 + - - +
615A ARG* 3.9 8.7 + - - +
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Residues in contact with THR 613 (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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609A HIS* 2.8 44.6 + - + +
610A PHE* 3.2 15.2 + - - +
612A ALA* 1.3 67.7 - - + +
614A LEU* 1.3 59.8 + - - +
615A ARG* 2.8 17.7 + - - +
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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