Contacts of the helix formed by residues 555 - 563 (chain M) in PDB entry 2GWS
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 555 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500M ALA* 3.5 14.0 - - - +
553M THR 4.0 1.2 - - - +
554M PRO* 1.3 87.2 - - + +
556M GLU* 1.3 65.1 + - - +
557M LYS* 3.3 19.5 + - - +
558M ASP* 3.0 37.3 + - - +
559M VAL* 3.6 3.3 + - - +
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Residues in contact with GLU 556 (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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419M ARG* 3.0 33.5 + - - -
500M ALA* 3.8 21.1 - - - +
503M LEU* 3.7 11.6 - - + +
504M LEU* 3.5 21.1 + - + -
555M THR* 1.3 74.4 - - - +
557M LYS* 1.3 64.0 + - - +
559M VAL* 2.9 19.7 + - - +
560M PHE* 3.2 19.8 + - + -
567M TYR* 3.6 15.7 + - + -
573M ARG* 2.8 43.8 + - - +
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Residues in contact with LYS 557 (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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555M THR* 3.1 11.0 + - - +
556M GLU* 1.3 78.9 - - - +
558M ASP* 1.3 57.8 + - - +
560M PHE* 3.1 5.8 + - - +
561M ARG* 2.8 30.6 + - - +
567M TYR* 3.6 53.9 + - + -
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Residues in contact with ASP 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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552M PRO 4.8 0.7 - - - +
553M THR* 3.9 17.9 - - + -
554M PRO* 3.2 21.1 - - + +
555M THR* 3.0 37.7 + - - +
557M LYS* 1.3 77.6 - - - +
559M VAL* 1.3 61.2 + - - +
561M ARG* 2.9 35.4 + - - +
562M LEU* 3.1 30.3 + - - +
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Residues in contact with VAL 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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500M ALA* 4.8 3.1 - - + -
501M CYS* 4.0 14.8 - - - +
504M LEU* 3.7 28.0 - - + -
516M MET* 4.5 3.4 - - + -
527M LEU* 4.2 14.8 - - + -
532M LEU* 4.2 6.7 - - + +
553M THR* 3.7 31.4 - - + +
555M THR 4.1 4.5 - - - +
556M GLU* 2.9 14.1 + - - +
558M ASP* 1.3 74.2 - - - +
560M PHE* 1.3 67.2 + - - +
562M LEU* 3.4 2.6 + - - +
563M LEU* 3.1 40.9 + - + +
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Residues in contact with PHE 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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504M LEU* 4.2 13.7 - - + -
512M PHE* 3.8 31.2 - + - -
516M MET* 3.9 17.3 - - + -
556M GLU 3.2 23.9 + - - -
557M LYS* 3.1 5.7 + - - +
559M VAL* 1.3 82.0 - - + +
561M ARG* 1.3 62.4 + - - +
563M LEU* 3.1 5.8 + - - -
564M GLY 2.9 5.0 + - - -
565M LEU* 2.9 47.0 + - + +
566M PRO 3.4 14.8 - - - -
567M TYR* 3.7 33.0 - + + +
568M ARG* 3.9 26.0 - - + -
573M ARG* 4.0 12.8 - - - -
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Residues in contact with ARG 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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552M PRO 5.2 2.2 + - - -
554M PRO* 5.6 1.2 - - - +
557M LYS 2.8 20.7 + - - +
558M ASP* 2.9 36.2 + - - +
559M VAL 3.3 0.2 - - - -
560M PHE* 1.3 73.0 - - - +
562M LEU* 1.3 87.2 + - - +
564M GLY* 2.9 20.1 + - - -
565M LEU 4.2 3.8 + - - -
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Residues in contact with LEU 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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523M LYS* 4.9 1.0 - - - +
525M MET* 3.6 16.7 - - - +
532M LEU* 3.6 26.5 - - + -
551M LEU* 4.1 21.8 - - + -
552M PRO* 3.8 23.1 - - + +
553M THR* 4.1 3.1 - - + -
558M ASP 3.1 17.6 + - - +
559M VAL 3.9 0.2 - - - +
561M ARG* 1.3 104.8 - - - +
563M LEU* 1.3 59.6 + - - +
564M GLY 3.1 1.2 + - - -
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Residues in contact with LEU 563 (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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516M MET* 3.7 44.0 - - + +
519M LEU* 3.8 20.7 - - + +
520M ALA* 4.0 17.7 - - + +
523M LYS* 3.0 29.4 - - + -
525M MET* 3.8 18.2 - - + -
527M LEU* 4.9 3.1 - - + -
532M LEU* 3.6 27.8 - - + -
559M VAL* 3.1 23.8 + - + +
560M PHE* 3.1 6.7 + - - +
562M LEU* 1.3 75.7 - - - +
564M GLY* 1.3 64.2 + - - +
565M LEU* 3.4 3.3 + - + +
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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