Contacts of the helix formed by residues 630 - 645 (chain U) 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 ASP 630 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594U GLY 4.7 8.3 + - - +
595U CYS* 5.6 0.2 - - - +
628U PHE 4.3 0.2 + - - -
629U LEU* 1.3 70.7 - - - +
631U PRO* 1.3 59.0 - - - +
632U ASN 3.3 0.9 - - - +
633U GLN* 3.3 12.1 + - + +
634U TYR* 2.9 27.4 + - - +
666U PHE 3.7 26.2 - - - +
668U ALA* 6.2 0.2 - - + -
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Residues in contact with PRO 631 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531U TRP* 3.9 4.8 - - + +
532U PRO* 3.0 35.8 - - + +
533U THR 4.6 2.9 - - - +
534U ARG* 4.6 10.1 - - - +
535U VAL* 4.9 3.6 - - + +
629U LEU 3.1 7.9 - - - +
630U ASP* 1.3 69.6 - - - +
632U ASN* 1.3 60.2 + - - +
634U TYR* 3.4 8.0 + - + +
635U GLN* 3.0 28.4 + - - +
668U ALA* 4.0 9.3 - - + -
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Residues in contact with ASN 632 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531U TRP* 4.3 4.0 - - - -
630U ASP* 3.3 0.8 - - - +
631U PRO* 1.3 72.5 - - - +
633U GLN* 1.3 26.1 - - - +
635U GLN* 3.3 2.6 + - - +
636U GLN* 3.1 17.5 + - - +
666U PHE 3.4 1.8 - - - +
667U LYS* 1.0 143.8 - - - +
668U ALA* 1.5 58.7 - - + +
669U VAL 2.9 1.1 - - - +
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Residues in contact with GLN 633 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426U LEU 5.0 1.6 - - - -
427U TYR* 4.5 1.7 - - - +
630U ASP* 3.3 20.9 + - + +
632U ASN* 1.3 20.7 - - - +
634U TYR* 1.3 62.8 + - - +
636U GLN* 3.8 3.5 - - - +
637U ASP* 3.0 25.0 + - - +
666U PHE* 4.4 9.2 - - + -
667U LYS* 1.2 94.1 - - - +
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Residues in contact with TYR 634 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532U PRO* 6.1 3.1 - - + -
535U VAL* 4.6 15.0 - - + -
629U LEU* 5.2 4.7 - - + -
630U ASP 2.9 17.0 + - - +
631U PRO* 3.6 10.1 - - + +
633U GLN* 1.3 78.3 - - - +
635U GLN* 1.3 57.4 + - - +
637U ASP* 3.4 5.9 + - - +
638U MET* 2.9 30.2 + - - +
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Residues in contact with GLN 635 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530U ASN 4.4 7.0 - - - +
531U TRP* 4.2 21.5 - - + -
532U PRO* 5.1 2.0 - - + -
631U PRO 3.0 16.7 + - - +
632U ASN* 3.8 4.7 - - - +
633U GLN 3.3 0.2 - - - -
634U TYR* 1.3 76.4 - - - +
636U GLN* 1.3 54.0 + - - +
638U MET* 3.3 5.9 + - - +
639U THR* 2.7 37.4 + - - -
667U LYS 5.4 0.7 - - - +
671U GLU* 5.7 4.3 - - + -
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Residues in contact with GLN 636 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426U LEU* 1.8 74.0 + - + +
427U TYR 3.1 10.2 + - - -
632U ASN 3.1 15.9 + - - +
633U GLN 3.8 3.1 - - - +
635U GLN* 1.3 77.3 - - - +
637U ASP* 1.3 55.8 + - - +
639U THR* 3.7 2.2 - - - -
640U ASN* 2.9 24.1 + - - +
667U LYS* 4.1 2.5 - - + -
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Residues in contact with ASP 637 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427U TYR* 2.7 28.9 - - + +
633U GLN 3.0 13.9 + - - +
634U TYR* 3.7 6.1 - - - +
636U GLN* 1.3 73.7 - - - +
638U MET* 1.3 57.1 + - - +
640U ASN* 3.3 2.9 + - - +
641U THR* 2.9 28.6 + - - -
646U ALA* 5.5 0.3 - - - +
647U GLU 5.4 1.6 - - - +
649U VAL* 5.0 17.3 - - + +
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Residues in contact with MET 638 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634U TYR 2.9 18.7 + - - +
635U GLN* 3.6 7.0 - - - +
637U ASP* 1.3 73.4 - - - +
639U THR* 1.3 54.3 + - - +
641U THR* 3.1 8.1 + - - -
642U ILE* 2.8 36.9 + - - +
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Residues in contact with THR 639 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425U PRO* 5.2 3.1 - - - -
426U LEU* 4.9 4.7 - - - -
635U GLN 2.7 21.4 + - - -
636U GLN* 3.7 8.1 - - - -
638U MET* 1.3 71.8 - - - +
640U ASN* 1.3 57.8 + - - +
642U ILE* 4.1 4.2 - - - +
643U GLN* 2.8 37.6 + - - +
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Residues in contact with ASN 640 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425U PRO* 3.2 34.9 - - + +
427U TYR* 4.3 10.5 - - + +
636U GLN 2.9 16.7 + - - +
637U ASP* 3.5 7.4 - - - +
639U THR* 1.3 76.0 - - - +
641U THR* 1.3 57.9 + - - +
643U GLN* 5.0 0.9 - - - -
644U ASN* 3.0 34.2 + - + +
646U ALA* 3.5 17.0 + - + +
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Residues in contact with THR 641 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637U ASP 2.9 13.9 + - - -
638U MET* 3.4 10.8 - - - -
640U ASN* 1.3 76.3 - - - +
642U ILE* 1.3 60.2 + - - +
645U GLY* 3.0 27.4 + - - -
646U ALA* 3.3 24.8 - - - +
647U GLU 4.7 7.0 - - - -
648U ASP* 5.0 7.6 - - - -
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Residues in contact with ILE 642 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638U MET 2.8 20.0 + - - +
639U THR* 4.1 4.5 - - - +
641U THR* 1.3 75.6 - - - +
643U GLN* 1.3 61.3 + - - +
645U GLY* 4.5 1.4 + - - -
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Residues in contact with GLN 643 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639U THR* 2.8 23.7 + - - +
640U ASN* 5.0 0.9 - - - -
642U ILE* 1.3 75.9 - - - +
644U ASN* 1.3 60.5 + - + +
645U GLY 3.7 0.8 + - - -
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Residues in contact with ASN 644 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425U PRO* 5.6 4.3 - - + -
640U ASN* 3.0 17.8 + - + +
643U GLN* 1.3 80.4 - - + +
645U GLY* 1.3 61.1 + - - +
646U ALA* 3.1 8.7 + - + +
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Residues in contact with GLY 645 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641U THR 3.0 14.0 + - - -
642U ILE 4.5 1.0 + - - -
643U GLN 3.7 1.4 - - - -
644U ASN* 1.3 77.2 - - - +
646U ALA* 1.3 66.2 + - - +
647U GLU* 3.6 1.7 + - - -
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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
------------------------------------------------------------
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