Contacts of the helix formed by residues 635 - 653 (chain M) in PDB entry 2DFS
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 THR 635 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510M ASP* 2.6 41.5 + - - +
513M CYS* 5.0 1.6 - - + -
568M ASN* 3.6 20.9 - - - +
569M LYS* 4.9 0.7 - - - -
570M ASP* 3.9 2.2 - - - -
633M LYS* 3.8 31.2 + - + +
634M LYS* 1.3 77.6 - - - +
636M VAL* 1.4 63.0 + - - +
637M GLY 4.3 0.9 - - - -
638M HIS* 3.2 16.0 - - - +
639M GLN* 2.8 31.5 + - - +
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Residues in contact with VAL 636 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244M LEU 5.6 1.3 - - - +
246M LYS* 4.5 26.7 - - + +
247M SER* 5.2 6.3 - - - +
405M LYS* 4.0 3.1 - - + +
449M PHE* 3.8 22.7 - - + -
567M LYS 3.4 21.1 - - - +
568M ASN* 2.9 19.3 + - - +
570M ASP* 3.5 26.0 - - + +
635M THR* 1.4 69.1 - - - +
637M GLY* 1.4 57.3 + - - +
639M GLN* 3.2 10.4 + - - +
640M PHE* 2.8 34.2 + - + +
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Residues in contact with GLY 637 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449M PHE* 3.8 10.0 - - - -
453M CYS* 5.5 1.1 - - - -
506M LEU* 4.6 26.9 - - - +
510M ASP* 4.9 2.5 - - - -
568M ASN* 2.8 21.9 + - - -
636M VAL* 1.4 72.1 - - - +
638M HIS* 1.3 54.1 + - - +
640M PHE* 3.3 8.1 + - - +
641M ARG* 3.0 28.8 + - - +
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Residues in contact with HIS 638 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510M ASP* 4.0 10.1 + - - +
633M LYS 5.5 1.6 - - - -
634M LYS* 2.8 49.6 + - + +
635M THR* 3.2 25.2 + - - +
636M VAL 3.5 0.2 - - - -
637M GLY* 1.3 73.6 - - - +
639M GLN* 1.3 62.8 + - + +
641M ARG* 3.4 8.2 + - - +
642M ASN* 3.0 52.2 + - - +
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Residues in contact with GLN 639 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246M LYS* 2.7 32.1 + - + +
570M ASP* 2.7 25.8 + - - +
634M LYS* 4.7 13.9 - - + +
635M THR 2.8 33.5 + - - +
636M VAL* 3.2 10.0 + - - +
638M HIS* 1.3 80.7 - - + +
640M PHE* 1.3 65.2 + - - +
642M ASN* 3.3 8.0 + - - +
643M SER* 3.0 24.7 + - - -
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Residues in contact with PHE 640 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243M LEU* 3.7 48.8 - - + +
244M LEU 4.9 6.7 - - - -
245M GLU* 6.4 0.4 - - + -
439M TYR* 3.7 17.0 - - - -
453M CYS* 3.1 54.3 - - + -
454M ILE* 4.4 0.9 - - + -
456M TYR* 3.9 22.9 - + - -
457M ALA* 4.2 7.6 - - + -
636M VAL* 2.8 25.1 + - + +
637M GLY* 3.3 9.4 + - - +
639M GLN* 1.3 71.1 - - - +
641M ARG* 1.3 57.0 + - - +
643M SER* 3.4 5.4 + - - -
644M LEU* 2.9 32.4 + - + +
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Residues in contact with ARG 641 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456M TYR* 3.2 25.3 - - + +
500M GLU* 2.6 58.5 + - - +
506M LEU* 5.2 5.6 - - + -
637M GLY 3.0 13.2 + - - +
638M HIS* 3.5 13.2 - - - +
639M GLN 3.3 0.2 - - - -
640M PHE* 1.3 76.1 - - - +
642M ASN* 1.3 63.8 + - - +
644M LEU* 3.4 4.7 + - - +
645M HIS* 3.0 49.1 + - + +
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Residues in contact with ASN 642 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634M LYS* 5.7 0.6 - - - +
638M HIS* 3.0 42.8 + - - +
639M GLN* 3.6 10.5 - - - +
641M ARG* 1.3 85.4 + - - +
643M SER* 1.3 60.7 + - - +
645M HIS* 3.5 5.2 + - - +
646M LEU* 3.2 35.1 + - + +
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Residues in contact with SER 643 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241M THR 4.8 0.3 + - - -
242M TYR* 3.5 16.2 - - - +
243M LEU* 3.1 32.1 + - - -
639M GLN 3.0 15.6 + - - -
640M PHE* 3.8 4.9 - - - -
642M ASN* 1.3 75.2 - - - +
644M LEU* 1.3 57.1 + - - +
646M LEU* 3.4 10.6 + - - +
647M LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 644 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243M LEU* 3.7 16.9 - - + +
456M TYR* 3.5 39.5 - - + +
457M ALA* 3.7 36.8 - - + +
460M LYS* 3.7 35.2 - - + -
461M LEU* 6.1 0.7 - - + -
640M PHE* 2.9 20.0 + - + +
641M ARG 3.5 5.4 - - - +
643M SER* 1.3 72.4 - - - +
645M HIS* 1.3 63.9 + - - +
647M LEU* 3.5 13.0 + - + +
648M MET* 3.1 30.9 + - + +
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Residues in contact with HIS 645 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460M LYS* 2.9 34.0 + - + -
500M GLU* 3.6 1.3 + - - -
641M ARG* 3.0 50.6 + - - +
642M ASN* 4.0 6.3 - - - +
643M SER 3.4 0.2 - - - -
644M LEU* 1.3 74.4 - - + +
646M LEU* 1.3 61.2 + - + +
648M MET* 3.0 11.9 + - + +
649M GLU* 2.9 53.1 + - - +
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Residues in contact with LEU 646 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242M TYR* 4.0 9.9 - - + -
642M ASN* 3.2 26.9 + - + +
643M SER* 3.6 8.1 - - - +
645M HIS* 1.3 77.6 - - + +
647M LEU* 1.3 60.3 + - - +
649M GLU* 3.6 21.0 + - - +
650M THR* 2.8 28.2 + - - -
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Residues in contact with LEU 647 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223M TYR* 5.5 2.0 - - + -
242M TYR* 3.6 40.0 - - + +
243M LEU* 4.0 28.9 - - + -
436M LEU* 4.2 16.2 - - + -
438M ILE* 4.1 15.5 - - + -
457M ALA* 6.1 0.2 - - + -
461M LEU* 5.2 4.0 - - + -
643M SER 3.0 17.9 + - - +
644M LEU* 3.5 14.1 - - + +
646M LEU* 1.3 75.1 - - - +
648M MET* 1.3 65.9 + - - +
650M THR* 3.3 5.6 + - - -
651M LEU* 3.0 50.8 + - + +
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Residues in contact with MET 648 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460M LYS* 3.4 50.3 - - + +
461M LEU* 4.0 24.2 - - + -
463M GLN* 4.5 6.7 - - - +
464M GLN* 3.9 31.9 - - + +
644M LEU* 3.1 17.5 + - + +
645M HIS* 3.0 16.8 + - + +
647M LEU* 1.3 79.9 - - - +
649M GLU* 1.3 55.9 + - + +
651M LEU* 3.3 7.5 + - + +
652M ASN* 2.8 46.5 + - - +
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Residues in contact with GLU 649 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645M HIS* 2.9 48.9 + - - +
646M LEU* 3.7 26.6 - - - +
647M LEU 3.4 0.2 - - - -
648M MET* 1.3 74.9 - - + +
650M THR* 1.3 61.9 + - - +
652M ASN* 3.3 14.3 + - - +
653M ALA* 3.4 13.0 + - - +
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Residues in contact with THR 650 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158M SER* 4.9 0.5 + - - -
223M TYR* 3.8 29.2 - - + -
225M GLU* 4.2 9.6 - - - +
240M ARG* 4.5 4.8 - - - +
242M TYR* 3.1 19.6 + - - +
432M PHE* 5.4 5.9 - - + -
646M LEU 2.8 19.5 + - - -
647M LEU* 3.5 8.1 - - - -
649M GLU* 1.3 77.3 - - - +
651M LEU* 1.3 61.9 + - - +
652M ASN 3.6 0.2 + - - -
653M ALA* 3.6 15.2 + - - +
654M THR* 3.9 11.6 - - - +
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Residues in contact with LEU 651 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158M SER* 3.6 26.0 - - - +
160M ILE* 4.3 9.9 - - + -
223M TYR* 4.2 19.3 - - + -
436M LEU* 3.9 15.0 - - + -
461M LEU* 3.7 29.4 - - + -
464M GLN* 2.8 27.0 + - - +
647M LEU* 3.0 41.3 + - + +
648M MET* 3.8 9.6 - - - +
649M GLU 3.3 0.2 - - - -
650M THR* 1.3 75.0 - - - +
652M ASN* 1.3 58.0 + - - +
653M ALA 3.4 0.7 - - - -
654M THR* 3.0 21.8 + - - +
656M PRO* 5.0 3.8 - - - +
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Residues in contact with ASN 652 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155M ARG* 3.7 10.0 + - - -
463M GLN* 6.0 0.6 - - - +
464M GLN* 2.9 28.7 + - - +
648M MET* 2.8 41.7 + - - +
649M GLU* 3.3 7.9 + - - +
651M LEU* 1.3 73.6 - - - +
653M ALA* 1.3 57.6 + - - +
654M THR 3.2 6.9 + - - -
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Residues in contact with ALA 653 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155M ARG* 3.4 22.2 + - - +
156M ASN* 4.5 10.2 + - - +
432M PHE* 6.2 2.0 - - + -
649M GLU 3.4 9.0 + - - +
650M THR* 3.8 12.1 - - - +
651M LEU 3.4 1.2 - - - -
652M ASN* 1.3 78.3 - - - +
654M THR* 1.3 59.6 + - + +
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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