Contacts of the helix formed by residues 641 - 652 (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 VAL 641 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A VAL* 3.6 20.5 - - + +
603A TRP 3.5 26.0 - - - +
604A ASN* 3.5 40.2 - - + +
608A ALA* 5.8 1.3 - - + -
636A ALA 3.8 5.3 + - - +
637A ALA* 3.6 20.6 + - + +
638A LEU 3.6 1.4 + - - -
639A PHE 4.1 0.2 - - - -
640A GLY* 1.3 76.3 - - - +
642A TYR* 1.3 88.7 + - + +
643A GLY 3.5 0.7 - - - -
644A PHE 3.9 0.2 + - - -
645A LEU* 3.3 22.1 + - + +
1001A HEM 4.6 4.7 - - + -
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Residues in contact with TYR 642 (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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343A ILE* 4.1 11.9 - - + +
347A PHE* 3.8 3.2 - - + -
493A VAL* 3.8 8.0 + - + -
494A GLU* 2.7 26.2 + - - -
497A PHE* 3.3 59.0 - + + +
498A GLU* 5.0 9.9 + - - -
531A PHE* 4.8 6.2 - - - -
604A ASN* 5.8 0.2 - - - -
637A ALA 4.0 3.8 - - - -
638A LEU* 2.8 20.7 + - + +
641A VAL* 1.3 89.5 - - + +
643A GLY* 1.3 58.1 + - - +
645A LEU* 3.4 12.4 - - + +
646A ALA* 2.8 30.1 + - - +
1001A HEM 2.9 46.1 - - + +
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Residues in contact with GLY 643 (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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342A TRP* 3.6 22.8 - - - -
343A ILE* 3.8 6.6 - - - +
638A LEU 2.8 14.3 + - - -
639A PHE* 3.4 18.5 + - - -
642A TYR* 1.3 69.9 - - - +
644A PHE* 1.3 59.4 + - - +
646A ALA* 3.2 4.5 + - - +
647A LEU* 2.8 34.0 + - - +
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Residues in contact with PHE 644 (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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596A CYS* 3.8 23.7 - - - +
597A PHE* 4.9 0.3 - - - -
599A ALA* 4.8 10.5 - - + -
600A VAL* 3.5 21.7 - - + +
603A TRP* 4.7 3.4 - + - -
639A PHE* 3.2 50.6 + + - +
640A GLY* 3.5 13.2 - - - -
641A VAL 3.9 1.5 + - - +
642A TYR 3.5 0.4 - - - -
643A GLY* 1.3 74.0 - - - +
645A LEU* 1.3 51.8 + - - +
647A LEU* 3.6 15.3 - - + +
648A GLY* 2.8 30.0 + - - -
672A PHE* 4.9 8.3 - + - -
675A LEU* 4.1 19.5 - - + -
676A ASN* 3.1 40.4 - - - -
679A LEU* 4.1 12.1 - - + -
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Residues in contact with LEU 645 (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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347A PHE* 3.6 25.8 - - + -
497A PHE* 4.2 18.8 - - + +
501A ALA* 4.6 4.3 - - + -
597A PHE* 4.2 21.5 - - + -
600A VAL* 3.7 21.7 - - + +
641A VAL* 3.3 16.9 + - + +
642A TYR* 3.4 24.0 - - + +
643A GLY 3.1 0.4 - - - -
644A PHE* 1.3 75.4 - - - +
646A ALA* 1.3 58.8 + - - +
648A GLY* 3.3 2.3 + - - -
649A PHE* 2.8 46.9 + - + +
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Residues in contact with ALA 646 (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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342A TRP* 3.8 20.6 - - + -
343A ILE* 4.4 7.9 - - + -
346A GLY* 4.1 13.2 - - - +
347A PHE* 3.6 22.9 - - + -
642A TYR 2.8 20.1 + - - +
643A GLY 3.2 4.5 + - - +
645A LEU* 1.3 72.9 - - - +
647A LEU* 1.3 57.8 + - - +
649A PHE* 3.3 3.4 + - - +
650A VAL* 2.8 33.9 + - - +
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Residues in contact with LEU 647 (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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288A VAL* 4.6 18.6 - - + -
291A PHE* 4.7 7.0 - - + -
342A TRP* 4.5 16.2 - - + -
596A CYS* 4.7 6.3 - - - -
639A PHE* 3.9 25.8 - - + -
643A GLY 2.8 19.3 + - - +
644A PHE* 3.6 18.8 - - + +
645A LEU 3.3 0.2 - - - -
646A ALA* 1.3 70.1 - - - +
648A GLY* 1.3 54.2 + - - +
650A VAL* 3.2 9.0 + - + +
651A LEU* 2.8 42.8 + - + +
675A LEU* 4.1 16.2 - - + -
738A VAL* 4.3 23.8 - - + -
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Residues in contact with GLY 648 (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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593A PRO* 5.4 4.7 - - - +
596A CYS* 4.3 6.8 - - - -
597A PHE* 4.1 20.4 - - - -
644A PHE 2.8 18.5 + - - -
645A LEU 3.6 3.4 - - - -
647A LEU* 1.3 71.3 - - - +
649A PHE* 1.3 62.4 + - - +
651A LEU* 3.4 13.9 + - - +
652A LEU* 2.8 25.8 + - - +
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Residues in contact with PHE 649 (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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284A VAL* 5.4 0.7 - - - +
346A GLY 4.1 7.6 - - - +
347A PHE* 3.6 35.7 - + - -
349A THR* 5.5 1.4 - - - +
350A ALA* 3.9 35.3 - - + +
354A LEU* 6.1 3.4 - - + -
500A PHE* 6.0 2.0 - + - -
501A ALA* 3.9 31.2 - - + -
504A ALA* 5.1 8.7 - - + -
505A PHE* 5.6 4.9 - + + -
597A PHE* 4.6 16.6 - + - -
645A LEU* 2.8 31.1 + - + +
646A ALA* 3.7 4.3 - - - +
648A GLY* 1.3 75.5 - - - +
650A VAL* 1.3 62.2 + - - +
652A LEU* 3.2 35.1 - - + +
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Residues in contact with VAL 650 (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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284A VAL* 3.7 41.9 - - + +
287A THR* 3.9 26.2 - - + -
288A VAL* 4.4 17.3 - - + -
346A GLY* 4.6 7.2 - - - +
349A THR* 4.9 0.9 - - + -
646A ALA 2.8 22.5 + - - +
647A LEU* 3.2 13.0 + - + +
649A PHE* 1.3 70.3 - - - +
651A LEU* 1.3 59.5 + - + +
654A ALA* 2.8 35.1 + - + +
742A ALA* 4.8 11.9 - - + -
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Residues in contact with LEU 651 (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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592A TRP* 3.7 25.6 - - + +
593A PRO* 5.0 10.8 - - + -
596A CYS* 4.5 12.6 - - - -
647A LEU* 2.8 24.4 + - + +
648A GLY* 3.5 13.5 - - - +
650A VAL* 1.3 79.5 - - + +
652A LEU* 1.3 51.5 + - - +
654A ALA* 3.6 6.2 - - + +
655A ARG* 2.8 41.6 + - + +
663A PHE* 4.4 16.2 - - + -
668A MET* 3.6 37.9 - - + -
741A GLN* 5.3 3.6 - - + -
742A ALA* 6.5 0.9 - - + -
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Residues in contact with LEU 652 (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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350A ALA* 6.1 2.7 - - + -
353A PHE* 3.7 28.7 - - + -
354A LEU* 4.0 36.6 - - + -
508A VAL* 4.5 21.5 - - + -
512A MET* 5.5 2.7 - - + -
590A LEU* 4.8 18.6 - - + -
593A PRO* 6.6 0.2 - - + -
597A PHE* 6.4 2.9 - - + -
648A GLY 2.8 16.2 + - - +
649A PHE* 3.2 36.1 + - + +
650A VAL 3.2 0.4 - - - -
651A LEU* 1.3 76.2 - - - +
654A ALA 2.6 24.1 + - - -
655A ARG* 3.7 10.0 + - + +
656A TYR* 4.5 24.3 + - + +
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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