Contacts of the helix formed by residues 686 - 701 (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 SER 686 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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681A GLY 4.0 2.0 + - - -
682A MET* 3.8 10.3 - - - -
684A ALA 3.3 0.2 - - - -
685A ILE* 1.3 83.5 - - - +
687A LEU* 1.3 68.8 + - - +
688A LEU 3.4 1.8 - - - -
689A PRO* 3.3 3.2 - - - +
690A VAL* 3.1 33.1 + - - +
720A LEU* 3.7 13.6 + - - -
721A ARG* 5.8 2.9 - - - -
724A ARG* 3.2 51.4 - - - +
727A ALA* 6.1 0.2 - - - +
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Residues in contact with LEU 687 (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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628A ASN* 3.9 17.6 - - + +
629A THR* 4.8 0.2 - - - -
631A ALA* 3.6 44.6 - - + +
632A VAL* 3.4 21.7 - - + +
635A HIS* 4.2 4.9 - - + +
682A MET* 3.4 22.7 + - + +
683A ILE* 4.4 7.1 - - + -
686A SER* 1.3 79.3 - - - +
688A LEU* 1.3 57.3 + - - +
690A VAL* 4.7 1.8 - - + -
691A GLY* 2.8 29.1 + - - +
721A ARG* 4.0 20.0 - - - +
724A ARG* 3.5 33.2 - - - +
1002A HEM 5.7 0.4 - - + -
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Residues in contact with LEU 688 (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* 5.4 15.0 - - + -
632A VAL* 4.2 6.0 - - + +
683A ILE 3.6 19.9 + - - +
684A ALA* 3.9 9.4 - - + +
687A LEU* 1.3 77.3 - - - +
689A PRO* 1.4 66.3 - - + +
691A GLY* 3.7 0.2 - - - -
692A VAL* 2.8 44.6 + - + +
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Residues in contact with PRO 689 (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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684A ALA 3.1 20.6 - - - +
685A ILE 3.1 22.2 - - - +
686A SER 3.3 10.3 - - - +
688A LEU* 1.4 90.1 - - + +
690A VAL* 1.3 51.0 + - - +
692A VAL* 3.4 10.1 - - + +
693A ILE* 2.8 47.7 + - + +
720A LEU* 3.8 14.8 - - + -
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Residues in contact with VAL 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A ASN* 3.1 31.0 - - + +
686A SER* 3.1 22.7 + - - +
687A LEU* 4.4 1.6 - - - +
689A PRO* 1.3 74.8 - - - +
691A GLY* 1.3 54.5 + - - +
693A ILE* 3.7 6.0 - - - +
694A GLN* 2.8 38.0 + - + +
712A LEU* 5.7 3.8 - - + -
717A LEU* 4.1 24.1 - - + +
720A LEU* 3.5 28.5 - - + -
721A ARG* 4.8 20.2 - - - +
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Residues in contact with GLY 691 (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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627A LEU* 4.5 0.2 - - - +
628A ASN* 4.0 5.4 - - - +
629A THR* 3.5 33.4 - - - +
687A LEU 2.8 25.3 + - - -
688A LEU 3.7 0.2 - - - -
690A VAL* 1.3 74.3 - - - +
692A VAL* 1.3 54.5 + - - +
694A GLN* 3.4 4.9 + - - +
695A ALA* 2.8 28.8 + - - +
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Residues in contact with VAL 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A THR* 4.4 2.6 - - - +
688A LEU* 2.8 35.3 + - + +
689A PRO* 3.4 12.1 - - + +
691A GLY* 1.3 69.2 - - - +
693A ILE* 1.3 61.3 + - + +
695A ALA* 3.5 8.5 - - + +
696A TYR* 2.8 56.5 + - + -
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Residues in contact with ILE 693 (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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689A PRO* 2.8 39.8 + - + +
690A VAL 3.7 3.6 - - - +
692A VAL* 1.3 74.1 - - + +
694A GLN* 1.3 54.6 + - - +
696A TYR* 3.2 7.8 + - - +
697A ALA* 2.8 34.0 + - - +
711A PHE* 3.8 21.5 - - + -
714A MET* 4.8 8.5 - - + -
716A ILE* 4.2 17.3 - - + -
717A LEU* 4.0 27.1 - - + -
720A LEU* 5.0 1.8 - - + -
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Residues in contact with GLN 694 (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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78A TYR* 5.6 4.2 + - - +
626A GLY 4.7 0.4 + - - -
627A LEU* 3.7 32.6 - - + +
628A ASN* 2.9 43.7 + - - +
690A VAL* 2.8 20.5 + - + +
691A GLY 3.5 4.3 - - - +
693A ILE* 1.3 74.7 - - - +
695A ALA* 1.3 52.1 + - - +
697A ALA 3.4 0.5 + - - -
698A SER* 2.8 35.5 + - - -
706A ALA* 3.4 28.7 + - + +
707A ARG* 4.0 13.9 - - - +
711A PHE* 3.9 15.3 - - + -
712A LEU* 4.3 12.1 - - - +
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Residues in contact with ALA 695 (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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623A TYR* 4.9 2.0 - - + +
624A ILE* 4.8 9.4 - - + -
627A LEU* 3.7 11.2 - - + +
629A THR* 4.6 7.6 - - + -
691A GLY 2.8 20.0 + - - +
692A VAL* 3.5 13.5 - - + +
693A ILE 3.3 0.2 - - - -
694A GLN* 1.3 70.6 - - - +
696A TYR* 1.3 59.4 + - + +
698A SER* 2.6 22.7 + - - -
699A ILE* 2.8 28.1 + - + +
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Residues in contact with TYR 696 (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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692A VAL* 2.8 46.1 + - + +
693A ILE* 3.7 6.5 - - - +
695A ALA* 1.3 70.0 - - + +
697A ALA* 1.3 59.9 + - - +
699A ILE* 3.2 24.9 + - + +
700A THR* 2.8 41.3 + - + +
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Residues in contact with ALA 697 (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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693A ILE 2.8 16.1 + - - +
694A GLN 3.6 2.9 - - - +
696A TYR* 1.3 72.4 - - - +
698A SER* 1.3 57.4 + - - +
700A THR* 3.6 6.5 - - - -
701A HIS* 2.8 33.6 + - - +
702A GLY 3.2 5.9 + - - +
705A TYR* 4.7 5.2 - - + -
706A ALA* 4.0 9.0 - - + -
711A PHE* 3.3 40.6 - - + -
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Residues in contact with SER 698 (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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217A HIS* 2.9 28.8 + - - -
623A TYR* 3.5 19.7 - - - +
627A LEU* 3.9 4.6 - - - +
694A GLN 2.8 17.3 + - - -
695A ALA* 2.6 27.7 + - - -
697A ALA* 1.3 70.0 - - - +
699A ILE* 1.3 62.0 + - - +
702A GLY* 3.4 15.8 - - - -
703A LEU* 4.1 22.2 - - - -
706A ALA* 3.5 10.9 - - - +
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Residues in contact with ILE 699 (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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217A HIS* 3.3 15.8 + - - -
623A TYR* 3.6 32.0 + - + +
695A ALA* 2.8 36.3 + - + +
696A TYR* 3.4 26.2 - - + +
698A SER* 1.3 74.2 + - - +
700A THR* 1.3 70.2 + - + +
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Residues in contact with THR 700 (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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217A HIS* 4.5 4.0 - - - -
219A PRO* 4.8 5.2 - - - +
696A TYR* 2.8 31.1 + - + +
697A ALA* 3.3 8.1 + - - -
699A ILE* 1.3 83.8 - - + +
701A HIS* 1.3 85.5 + - - +
702A GLY 3.3 0.9 + - - -
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Residues in contact with HIS 701 (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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219A PRO* 4.6 4.6 - - - +
697A ALA* 2.8 6.9 + - - +
700A THR* 1.3 92.7 + - - +
702A GLY* 1.3 57.8 + - - +
704A TRP* 3.2 28.2 - - + -
705A TYR* 3.3 54.3 - + + -
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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