Contacts of the helix formed by residues 553 - 562 (chain M) in PDB entry 6KW5
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 ILE 553 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337M GLU* 3.8 30.1 - - + +
341M PRO* 3.7 17.0 - - + -
534M LEU* 4.5 15.5 - - + -
549M PHE* 3.2 50.9 - - + +
550M CYS* 4.7 1.3 - - - +
551M GLN 3.3 0.2 - - - -
552M ARG* 1.3 84.2 - - + +
554M ARG* 1.3 62.8 + - - +
555M PRO* 3.5 2.5 - - - -
556M LEU* 3.1 10.9 + - + +
557M VAL* 2.9 44.1 + - + +
574M TYR* 3.7 9.6 - - + +
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Residues in contact with ARG 554 (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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466D GLU* 4.5 15.2 + - - -
258I LYS* 4.8 10.5 - - - +
261I LEU* 4.1 24.4 - - - +
550M CYS 4.2 2.7 - - - +
551M GLN* 4.0 14.6 + - - +
553M ILE* 1.3 77.7 - - - +
555M PRO* 1.4 64.5 - - + +
557M VAL* 4.5 3.1 - - - +
558M LEU* 2.9 49.6 + - + +
574M TYR* 3.1 26.6 + - + +
575M MET* 4.7 18.8 - - + -
578M THR* 4.2 34.0 - - - +
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Residues in contact with PRO 555 (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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462D VAL* 3.9 21.8 - - + -
466D GLU* 3.9 25.0 - - - +
254I TYR* 5.6 0.5 + - - -
551M GLN 3.8 12.8 - - - +
552M ARG* 4.3 4.3 - - - +
553M ILE 3.7 5.4 - - - +
554M ARG* 1.4 95.5 - - + +
556M LEU* 1.3 57.2 + - + +
558M LEU* 4.1 9.7 - - + +
559M HIS* 4.2 22.0 + - - -
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Residues in contact with LEU 556 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I ILE* 3.7 48.7 - - + +
337M GLU 4.4 7.6 - - - +
341M PRO* 3.7 29.2 - - + -
552M ARG 5.7 1.1 - - - +
553M ILE* 3.1 12.9 + - + +
554M ARG 3.1 0.6 - - - -
555M PRO* 1.3 76.9 - - - +
557M VAL* 1.3 65.3 + - - +
558M LEU 3.2 1.3 - - - -
559M HIS* 3.5 19.5 + - + +
560M LYS* 3.7 18.6 + - - +
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Residues in contact with VAL 557 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341M PRO* 4.1 12.1 - - + -
344M LEU* 3.9 20.6 - - + -
534M LEU* 5.0 4.5 - - + -
553M ILE* 2.9 39.3 + - + +
554M ARG* 4.2 4.0 - - - +
556M LEU* 1.3 73.7 - - - +
558M LEU* 1.3 59.3 + - - +
559M HIS 3.2 0.7 - - - -
560M LYS* 2.9 21.5 + - - +
561M LEU* 2.9 32.5 + - + +
571M LEU* 3.9 16.8 - - + -
574M TYR* 4.5 16.2 - - + -
575M MET* 6.1 1.6 - - + -
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Residues in contact with LEU 558 (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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466D GLU* 4.5 10.1 - - - +
254I TYR* 3.4 35.1 - - + +
257I TYR* 4.2 14.4 - - + -
258I LYS* 4.2 21.8 - - + +
261I LEU* 3.8 29.2 - - + -
554M ARG* 2.9 35.1 + - + +
555M PRO* 4.3 7.4 - - + +
556M LEU 3.2 0.2 - - - -
557M VAL* 1.3 78.2 - - - +
559M HIS* 1.3 60.4 + - - +
561M LEU* 3.6 5.3 + - + +
562M ALA* 3.5 18.7 + - - +
575M MET* 4.8 11.7 - - + -
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Residues in contact with HIS 559 (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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254I TYR* 3.5 42.7 + + + -
555M PRO 4.2 16.7 + - - -
556M LEU* 3.5 17.5 + - + +
557M VAL 3.2 0.8 - - - -
558M LEU* 1.3 76.7 - - - +
560M LYS* 1.3 64.8 + - + +
562M ALA* 3.6 11.6 + - - +
563M ASP* 3.5 19.9 + - - +
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Residues in contact with LYS 560 (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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56I ILE* 5.1 12.2 - - - +
341M PRO* 2.5 45.3 + - + +
342M ASN* 3.5 12.9 + - - +
344M LEU* 4.9 6.7 - - + -
345M SER* 3.7 28.7 + - - +
556M LEU* 3.7 18.8 - - - +
557M VAL* 2.9 13.0 + - - +
559M HIS* 1.3 80.0 - - - +
561M LEU* 1.3 63.2 + - + +
563M ASP* 3.4 9.6 + - + +
564M ILE* 3.3 19.7 + - + +
567M LEU* 3.4 23.3 - - + +
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Residues in contact with LEU 561 (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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257I TYR* 3.3 44.6 - - + +
332I LEU* 5.6 1.9 - - - +
557M VAL* 2.9 43.6 + - + +
558M LEU* 4.1 5.8 - - + +
559M HIS 3.4 0.2 - - - -
560M LYS* 1.3 74.8 - - - +
562M ALA* 1.3 63.5 + - - +
563M ASP 3.2 0.6 + - - -
564M ILE 3.5 17.7 + - - +
565M PRO* 4.6 1.4 - - - +
567M LEU* 3.3 29.6 - - + +
568M THR* 4.7 4.8 + - - +
571M LEU* 3.7 22.9 - - + +
575M MET* 3.7 28.5 - - + -
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Residues in contact with ALA 562 (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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253I VAL* 3.4 26.0 - - + +
254I TYR* 4.3 30.1 - - + -
257I TYR* 4.4 17.7 - - + -
336I VAL* 4.8 6.4 - - - +
519M PHE* 5.7 1.4 - - - -
558M LEU 3.5 11.2 + - - +
559M HIS* 3.9 9.6 - - - +
560M LYS 3.3 0.6 - - - -
561M LEU* 1.3 78.7 - - - +
563M ASP* 1.3 63.9 + - - +
565M PRO* 5.5 1.1 - - - +
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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