Contacts of the helix formed by residues 608 - 616 (chain A) in PDB entry 6FWF
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 ALA 608 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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567A LEU* 3.4 17.5 - - + -
603A TRP 4.3 2.0 + - - +
604A ASN* 4.5 4.9 + - - +
606A ILE 3.3 0.2 - - - -
607A GLY* 1.3 77.8 - - - +
609A GLY* 1.3 63.3 + - - +
612A GLY* 2.8 29.6 + - - +
637A ALA* 4.6 2.4 - - + +
641A VAL* 5.8 0.7 - - + -
1001A HEM 3.2 57.4 - - + +
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Residues in contact with GLY 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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564A VAL* 3.8 20.7 - - - +
567A LEU* 3.7 24.3 - - - +
568A VAL* 6.4 0.2 - - - -
604A ASN 4.0 0.6 + - - -
605A MET* 3.5 11.5 + - - -
608A ALA* 1.3 81.6 - - - +
610A VAL* 1.3 60.7 + - - +
613A PHE* 3.3 22.9 - - - +
1001A HEM 4.5 3.1 - - - -
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Residues in contact with VAL 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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564A VAL* 6.0 2.0 - - + -
568A VAL* 5.9 5.6 - - + -
605A MET* 3.3 19.9 + - + +
606A ILE* 3.2 28.5 - - + +
609A GLY* 1.3 77.3 - - - +
611A PHE* 1.3 72.2 + - + +
613A PHE* 4.6 2.0 - - - -
614A LEU* 3.6 19.5 + - - +
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Residues in contact with PHE 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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606A ILE* 3.1 36.4 + - + +
607A GLY* 3.3 21.5 - - - +
610A VAL* 1.3 84.9 - - + +
612A GLY* 1.3 64.6 + - - +
613A PHE 3.4 0.2 - - - -
614A LEU* 3.4 33.5 - - + +
615A ILE* 3.6 17.3 + - + +
629A THR 5.3 2.5 - - - -
632A VAL* 3.4 37.7 - - + -
633A HIS* 4.2 11.4 + - + +
636A ALA* 6.1 1.3 - - + -
683A ILE* 5.5 6.1 - - + -
688A LEU* 5.4 14.6 - - + -
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Residues in contact with GLY 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 ALA 2.8 18.0 + - - -
611A PHE* 1.3 80.3 - - - +
613A PHE* 1.3 51.1 + - - +
615A ILE 3.4 1.4 + - - -
616A ASN 2.8 27.7 + - - -
633A HIS* 3.8 7.9 + - - -
1001A HEM 3.0 41.4 - - - +
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Residues in contact with PHE 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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233A SER 5.0 0.7 - - - -
236A SER* 3.8 18.6 - - - -
237A VAL* 3.8 29.6 - - + -
240A LEU* 4.2 19.5 - - + -
560A SER 4.4 1.3 - - - -
561A ALA* 3.6 20.4 - - + -
564A VAL* 3.8 18.2 - - + -
608A ALA 3.6 0.8 + - - -
609A GLY 3.3 18.7 + - - +
610A VAL* 5.0 2.0 - - - -
611A PHE 3.4 0.2 - - - -
612A GLY* 1.3 71.7 - - - +
614A LEU* 1.3 63.2 + - - +
615A ILE 3.3 0.4 - - - -
616A ASN* 3.2 33.0 - - + -
617A PRO* 3.1 22.1 - - + +
1001A HEM 3.1 9.9 - - + +
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Residues in contact with LEU 614 (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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610A VAL 3.6 16.1 + - - +
611A PHE* 3.4 36.3 + - + +
613A PHE* 1.3 79.6 - - - +
615A ILE* 1.3 66.9 + - + +
617A PRO* 3.5 10.6 - - - +
620A SER* 3.8 19.8 - - - +
624A ILE* 5.1 6.1 - - + -
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Residues in contact with ILE 615 (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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611A PHE* 3.6 14.1 + - + +
612A GLY 3.4 3.1 + - - +
613A PHE 3.3 0.2 - - - -
614A LEU* 1.3 83.7 - - + +
616A ASN* 1.3 64.1 + - - +
617A PRO* 3.4 2.9 - - - -
620A SER* 4.9 2.0 - - - -
621A LEU* 3.2 39.0 - - + +
624A ILE* 3.4 42.8 - - + -
629A THR* 4.2 18.4 - - - +
630A SER* 3.7 14.6 - - - +
633A HIS* 4.9 7.2 - - + -
1001A HEM 3.2 32.5 - - + +
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Residues in contact with ASN 616 (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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236A SER* 4.6 4.9 + - - -
541A HIS* 3.6 5.8 - - - +
544A TYR* 3.3 28.4 + - - -
557A ALA* 3.7 10.1 + - - +
560A SER* 2.6 37.6 + - - -
612A GLY 2.8 17.3 + - - +
613A PHE* 3.2 38.9 - - + -
615A ILE* 1.3 78.2 - - - +
617A PRO* 1.3 69.7 - - + +
618A PRO* 3.5 0.5 - - - +
621A LEU* 4.4 0.5 - - - +
1001A HEM 3.7 11.4 - - + -
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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