Contacts of the helix formed by residues 618 - 637 (chain q) in PDB entry 6FF7
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 GLY 618 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616q LEU* 3.8 1.0 - - - +
617q THR* 1.3 81.6 + - - +
619q GLN* 1.3 54.3 + - - -
620q GLU 3.4 2.5 - - - -
621q GLU* 3.3 8.5 + - - +
622q ILE* 2.8 37.5 + - - +
649q TYR* 5.1 4.0 - - - -
675q THR* 5.3 3.3 - - - -
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Residues in contact with GLN 619 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618q GLY* 1.3 68.5 - - - -
620q GLU* 1.3 56.9 + - - +
622q ILE* 3.1 6.9 + - - +
623q GLU* 2.7 37.5 + - - +
649q TYR* 4.6 18.0 - - + +
651q ASN* 6.0 5.8 - - + -
853q SER* 6.5 0.4 - - - -
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Residues in contact with GLU 620 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618q GLY 3.4 0.4 - - - -
619q GLN* 1.3 78.9 - - - +
621q GLU* 1.3 64.4 + - - +
623q GLU* 3.3 6.6 + - - +
624q ALA* 3.0 23.6 + - - +
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Residues in contact with GLU 621 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616q LEU* 5.0 9.2 - - + -
617q THR* 5.1 6.3 - - - +
618q GLY* 3.3 16.9 + - - +
619q GLN 3.2 0.4 - - - -
620q GLU* 1.3 78.5 - - - +
622q ILE* 1.3 63.7 + - - +
624q ALA* 3.2 8.8 + - - +
625q ALA* 3.0 22.7 + - - +
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Residues in contact with ILE 622 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616q LEU* 4.8 13.4 - - + +
618q GLY 2.8 19.8 + - - +
619q GLN* 3.1 6.9 + - - +
621q GLU* 1.3 77.2 - - - +
623q GLU* 1.3 57.4 + - - +
625q ALA* 3.1 8.4 + - - +
626q CYS* 2.8 29.2 + - - +
647q PRO* 4.9 12.3 - - + +
648q ILE 5.4 5.2 - - - +
649q TYR* 5.6 2.9 - - + -
673q VAL* 4.8 20.0 - - + +
674q ALA 6.2 1.1 - - - -
675q THR 6.3 0.2 - - - +
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Residues in contact with GLU 623 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619q GLN 2.7 20.6 + - - +
620q GLU* 3.6 7.2 - - - +
622q ILE* 1.3 72.8 - - - +
624q ALA* 1.3 62.9 + - - +
626q CYS* 3.3 8.5 + - - +
627q GLU* 3.2 21.7 + - - +
647q PRO* 5.4 4.2 - - - +
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Residues in contact with ALA 624 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620q GLU 3.0 14.2 + - - +
621q GLU* 3.4 11.4 - - - +
622q ILE 3.1 0.2 - - - -
623q GLU* 1.3 76.0 - - - +
625q ALA* 1.3 62.2 + - - +
627q GLU* 3.3 7.8 + - - +
628q MET* 3.1 22.8 + - - +
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Residues in contact with ALA 625 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593q LEU* 6.4 1.8 - - + -
597q VAL* 6.5 0.9 - - + -
621q GLU 3.0 13.1 + - - +
622q ILE* 3.1 11.0 + - - +
624q ALA* 1.3 72.2 - - - +
626q CYS* 1.3 61.6 + - - +
628q MET* 3.9 5.3 - - - +
629q LEU* 2.8 34.9 + - + +
673q VAL* 5.1 9.6 - - + -
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Residues in contact with CYS 626 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622q ILE 2.8 13.3 + - - +
623q GLU* 3.6 12.3 - - - +
625q ALA* 1.3 77.7 - - - +
627q GLU* 1.3 57.5 + - - +
629q LEU* 4.0 3.4 - - - +
630q GLN* 2.9 33.6 + - - +
645q VAL* 4.6 14.7 - - + +
646q LEU 5.7 0.9 - - - -
647q PRO* 5.1 16.4 - - + -
673q VAL* 5.6 5.1 - - + +
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Residues in contact with GLU 627 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623q GLU 3.2 9.4 + - - +
624q ALA* 3.7 8.7 - - - +
625q ALA 3.2 0.2 - - - -
626q CYS* 1.3 80.4 - - - +
628q MET* 1.3 57.9 + - - +
630q GLN* 3.7 5.0 - - - +
631q ASP* 2.9 31.8 + - - +
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Residues in contact with MET 628 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597q VAL* 5.6 9.4 - - + -
624q ALA 3.1 16.1 + - - +
625q ALA* 3.9 5.2 - - - +
627q GLU* 1.3 76.2 - - - +
629q LEU* 1.3 59.3 + - - +
631q ASP* 3.3 6.1 + - - +
632q ARG* 2.9 30.0 + - - +
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Residues in contact with LEU 629 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597q VAL* 5.9 8.0 - - + +
600q VAL* 5.9 7.4 - - + -
625q ALA* 2.8 18.6 + - + +
626q CYS* 4.0 3.8 - - - +
628q MET* 1.3 73.4 - - - +
630q GLN* 1.3 56.9 + - - +
632q ARG* 3.3 5.0 + - - +
633q CYS* 2.8 36.3 + - - +
645q VAL* 5.0 9.4 - - + -
671q VAL* 6.1 3.8 - - + -
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Residues in contact with GLN 630 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626q CYS 2.9 21.2 + - - +
627q GLU* 3.7 5.4 - - - +
629q LEU* 1.3 77.1 - - - +
631q ASP* 1.3 61.2 + - - +
633q CYS* 3.2 6.8 + - - +
634q ARG* 3.0 23.0 + - - +
643q LEU 5.6 2.7 - - - -
645q VAL* 4.9 12.8 - - + +
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Residues in contact with ASP 631 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627q GLU 2.9 18.5 + - - +
628q MET* 3.7 5.8 - - - +
630q GLN* 1.3 77.2 - - - +
632q ARG* 1.3 61.6 + - - +
634q ARG* 3.2 9.3 + - - +
635q ARG* 3.1 19.4 + - - +
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Residues in contact with ARG 632 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601q LEU* 5.5 11.0 - - + -
628q MET 2.9 17.4 + - - +
629q LEU* 3.7 5.6 - - - +
631q ASP* 1.3 74.6 - - - +
633q CYS* 1.3 66.0 + - - +
635q ARG* 3.0 11.3 + - - +
636q LEU* 2.9 20.4 + - - +
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Residues in contact with CYS 633 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629q LEU 2.8 18.7 + - - +
630q GLN* 3.5 7.2 - - - +
632q ARG* 1.3 77.8 - - - +
634q ARG* 1.3 63.3 + - - +
636q LEU* 2.9 20.6 + - - +
637q GLY* 2.9 10.0 + - - -
643q LEU* 3.9 38.4 - - + +
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Residues in contact with ARG 634 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630q GLN 3.0 9.4 + - - +
631q ASP* 3.2 11.2 + - - +
633q CYS* 1.3 78.9 - - - +
635q ARG* 1.3 58.2 + - - +
637q GLY* 2.9 24.8 - - - +
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Residues in contact with ARG 635 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631q ASP 3.1 11.1 + - - +
632q ARG* 3.0 15.6 + - - +
634q ARG* 1.3 74.8 - - - +
636q LEU* 1.3 66.9 + - - +
637q GLY* 3.3 0.9 + - - -
638q SER 4.7 1.0 + - - -
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Residues in contact with LEU 636 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605q VAL* 6.6 0.2 - - + -
632q ARG 2.9 10.3 + - - +
633q CYS* 2.9 14.9 + - - +
635q ARG* 1.3 77.6 - - - +
637q GLY* 1.3 66.8 + - - +
638q SER* 3.0 4.3 + - - -
639q LYS* 3.1 17.0 + - - +
640q ILE* 3.6 25.1 + - + -
641q ARG 5.6 0.9 - - - +
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Residues in contact with GLY 637 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633q CYS 2.9 8.1 + - - -
634q ARG* 2.9 22.8 + - - -
635q ARG 4.0 0.4 - - - -
636q LEU* 1.3 73.8 - - - +
638q SER* 1.3 60.7 + - - +
640q ILE 2.5 29.2 + - - +
641q ARG 5.5 0.9 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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