Contacts of the helix formed by residues 628 - 642 (chain M) 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 GLN 628 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624M GLU* 3.6 20.5 - - + +
626M ALA* 3.2 10.9 - - + +
627M GLN* 1.3 78.7 - - - +
629M TYR* 1.3 64.8 + - - +
630M ASP* 3.3 14.8 + - + +
631M MET* 3.8 1.8 + - + +
632M PHE* 3.8 10.0 + - - +
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Residues in contact with TYR 629 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627M GLN 3.9 1.4 + - - -
628M GLN* 1.3 70.6 - - - +
630M ASP* 1.3 59.3 + - - +
632M PHE* 3.5 11.4 - - + +
633M ASN* 2.9 31.2 + - - +
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Residues in contact with ASP 630 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628M GLN* 3.1 10.0 - - + +
629M TYR* 1.3 79.4 - - - +
631M MET* 1.3 59.8 + - - +
633M ASN* 3.1 5.3 + - - +
634M ILE* 2.9 26.6 + - - +
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Residues in contact with MET 631 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623M VAL* 3.6 45.0 - - + +
624M GLU* 3.8 10.8 - - + -
628M GLN* 3.8 3.6 + - + +
630M ASP* 1.3 79.4 - - - +
632M PHE* 1.3 56.3 + - - +
634M ILE* 3.6 9.1 - - - +
635M TYR* 2.9 30.0 + - - +
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Residues in contact with PHE 632 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624M GLU* 5.1 0.6 - - - +
628M GLN 3.8 5.9 + - - +
629M TYR* 3.4 20.1 + - + +
630M ASP 3.1 0.8 - - - -
631M MET* 1.3 79.0 - - - +
633M ASN* 1.3 56.5 + - - +
635M TYR* 3.3 5.7 + - - +
636M ILE* 2.9 29.5 + - - +
655M ALA* 6.2 4.0 - - + -
663M HIS* 6.5 0.7 - - + -
667M MET* 6.0 6.1 - - + -
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Residues in contact with ASN 633 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629M TYR 2.9 17.6 + - - +
630M ASP* 3.7 4.9 - - - +
632M PHE* 1.3 75.3 - - - +
634M ILE* 1.3 59.4 + - - +
636M ILE* 4.2 6.0 - - - +
637M LYS* 2.9 31.1 + - - +
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Residues in contact with ILE 634 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630M ASP 2.9 13.4 + - - +
631M MET* 3.6 12.3 - - - +
632M PHE 3.2 0.4 - - - -
633M ASN* 1.3 79.6 - - - +
635M TYR* 1.3 58.6 + - - +
637M LYS* 4.0 4.1 - - - +
638M ARG* 2.9 28.8 + - - +
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Residues in contact with TYR 635 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616M TYR* 5.4 2.5 - - - +
620M THR* 4.6 22.7 - - - -
623M VAL* 5.6 2.5 - - + -
631M MET 2.9 16.5 + - - +
632M PHE* 3.9 4.9 - - - +
634M ILE* 1.3 75.4 - - - +
636M ILE* 1.3 59.7 + - - +
638M ARG* 3.7 6.2 - - - +
639M ALA* 2.9 30.5 + - - +
651M ILE* 5.2 2.6 - - + +
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Residues in contact with ILE 636 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632M PHE 2.9 17.8 + - - +
633M ASN* 4.2 6.5 - - - +
635M TYR* 1.3 77.4 - - - +
637M LYS* 1.3 58.5 + - - +
639M ALA* 3.5 6.3 + - - +
640M ALA* 2.9 27.2 + - - +
651M ILE* 4.9 10.8 - - + -
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Residues in contact with LYS 637 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633M ASN 2.9 21.3 + - - +
634M ILE* 4.0 4.9 - - - +
636M ILE* 1.3 75.7 - - - +
638M ARG* 1.3 58.5 + - - +
640M ALA* 3.4 7.9 - - - +
641M GLU* 2.9 32.1 + - - +
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Residues in contact with ARG 638 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616M TYR* 4.9 17.9 - - + -
634M ILE 2.9 20.4 + - - +
635M TYR* 3.7 7.9 - - - +
637M LYS* 1.3 75.7 - - - +
639M ALA* 1.3 61.2 + - - +
641M GLU* 3.8 3.6 + - - +
642M ILE* 3.5 24.4 + - - +
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Residues in contact with ALA 639 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635M TYR 2.9 16.9 + - - +
636M ILE 3.7 4.3 - - - +
638M ARG* 1.3 75.8 - - - +
640M ALA* 1.3 57.3 + - - +
642M ILE 2.8 21.7 - - - +
643M TYR* 5.7 0.4 - - - -
644M GLY* 4.3 6.1 - - - +
647M HIS* 4.2 33.8 - - + +
648M THR* 4.8 5.8 + - - +
651M ILE* 4.3 12.6 - - + -
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Residues in contact with ALA 640 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636M ILE 2.9 19.4 + - - +
637M LYS* 3.0 10.5 + - - +
639M ALA* 1.3 79.2 - - - +
641M GLU* 1.3 61.6 + - - +
642M ILE 3.2 3.8 + - - +
644M GLY* 5.7 1.9 + - - -
648M THR* 6.0 3.6 - - - -
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Residues in contact with GLU 641 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637M LYS 2.9 13.5 + - - +
638M ARG* 3.8 4.5 + - - +
639M ALA 3.6 0.2 - - - -
640M ALA* 1.3 77.3 - - - +
642M ILE* 1.3 58.5 + - + +
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Residues in contact with ILE 642 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638M ARG 3.5 15.1 + - - +
639M ALA* 2.8 22.5 - - - +
640M ALA 3.9 2.9 - - - +
641M GLU* 1.3 78.1 - - + +
643M TYR* 1.3 73.0 + - + +
644M GLY 3.1 0.3 + - - -
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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