Contacts of the helix formed by residues 554 - 566 (chain M) in PDB entry 4G7Z
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 554 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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553M ASP* 1.3 73.6 - - - +
555M ALA* 1.3 71.8 + - - +
556M ASN* 3.3 36.6 + - - +
557M ARG* 3.1 9.3 + - + +
558M ALA* 3.1 17.8 + - - +
879M ARG 3.8 15.1 - - - +
880M MET* 3.1 39.5 + - + +
881M ASN* 4.2 1.2 - - - +
1042N ARG* 3.5 23.6 + - - -
1061N PHE* 3.5 16.9 - - + -
1070N TYR* 3.8 0.2 - - - -
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Residues in contact with ALA 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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441M VAL* 4.4 9.1 - - + +
553M ASP 3.7 0.4 + - - -
554M ASP* 1.3 76.4 + - - +
556M ASN* 1.3 64.1 + - - +
558M ALA* 3.1 12.9 + - - +
559M LEU* 3.1 12.6 + - - +
1042N ARG* 5.4 3.4 - - - +
1061N PHE* 5.1 0.6 - - - -
1070N TYR* 3.5 28.2 + - + +
1073N SER* 5.3 7.0 - - - -
1074N SER* 4.9 14.8 - - - +
1077N ALA* 4.1 21.1 - - + -
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Residues in contact with ASN 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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554M ASP* 3.2 23.3 + - - +
555M ALA* 1.3 75.1 - - - +
557M ARG* 1.3 63.2 + - - +
559M LEU* 3.3 22.0 - - - +
560M MET* 3.9 10.8 + - - +
1042N ARG* 5.6 1.2 - - - +
1077N ALA* 3.8 36.6 - - - +
1081N GLY* 5.7 1.4 + - - -
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Residues in contact with ARG 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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554M ASP* 3.1 9.5 + - - +
556M ASN* 1.3 76.9 - - - +
558M ALA* 1.3 65.9 + - - +
559M LEU 3.1 1.8 - - - -
560M MET* 3.0 35.7 + - - +
561M GLY 3.0 16.8 + - - -
686M ASP* 4.6 4.9 + - - -
843M HIS 3.6 19.3 - - - +
844M GLY* 3.3 27.2 + - - -
845M ASN* 5.3 1.0 - - - +
846M LYS* 4.3 12.7 - - - +
879M ARG* 3.5 63.1 - - + +
881M ASN* 3.7 24.9 - - + +
741N ASP* 6.1 0.4 - - - +
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Residues in contact with ALA 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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441M VAL* 3.6 10.5 - - + -
547M ILE* 3.4 10.1 - - + +
550M LEU* 3.5 20.2 - - + -
553M ASP* 4.6 6.2 - - + +
554M ASP 3.1 7.3 + - - +
555M ALA 3.1 9.4 + - - +
557M ARG* 1.3 76.8 - - - +
559M LEU* 1.3 56.6 + - - +
561M GLY* 3.1 1.4 + - - +
562M SER* 2.9 32.7 + - - -
843M HIS* 4.6 4.0 + - - +
1070N TYR* 3.5 22.9 - - - +
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Residues in contact with LEU 559 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441M VAL* 3.5 29.5 - - - +
443M THR* 3.2 36.8 - - + +
444M PRO 4.6 3.8 - - - +
445M GLU* 3.9 24.7 - - + -
449M ILE* 5.2 5.8 - - + -
555M ALA 3.1 10.1 + - - +
556M ASN* 3.3 16.4 - - - +
558M ALA* 1.3 76.5 - - - +
560M MET* 1.3 70.1 + - + +
562M SER* 3.3 3.3 + - - -
563M ASN* 2.8 49.9 + - + +
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Residues in contact with MET 560 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445M GLU* 3.2 38.1 - - - +
556M ASN 4.2 7.6 - - - +
557M ARG* 3.0 48.0 + - - +
559M LEU* 1.3 86.2 - - + +
561M GLY* 1.3 60.5 + - - +
563M ASN* 4.4 3.8 - - - +
564M MET* 2.9 53.6 + - + +
844M GLY* 4.2 4.0 - - - +
846M LYS* 3.3 31.6 - - - +
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Residues in contact with GLY 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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547M ILE* 3.9 5.2 - - - -
557M ARG 3.0 10.8 + - - -
558M ALA 3.1 4.6 + - - -
560M MET* 1.3 80.0 - - - +
562M SER* 1.3 64.5 + - - +
564M MET* 4.1 0.9 - - - +
565M GLN* 3.1 25.0 + - - +
841M ASN 4.5 3.7 - - - +
842M ARG* 3.3 28.8 - - - -
844M GLY* 3.9 6.8 - - - -
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Residues in contact with SER 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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441M VAL* 3.7 2.1 - - - +
442M GLU* 4.2 13.9 - - - -
543M ASN* 2.9 44.5 + - - -
544M THR* 2.9 35.3 + - - +
547M ILE* 3.6 1.9 - - - +
558M ALA 2.9 12.7 + - - -
559M LEU* 3.5 7.0 - - - -
561M GLY* 1.3 77.9 - - - +
563M ASN* 1.3 63.1 + - - +
564M MET 3.2 0.3 + - - -
565M GLN* 3.2 10.8 + - - +
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Residues in contact with ASN 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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405M ARG* 3.2 23.4 + - - +
409M ARG* 3.5 13.2 + - - -
442M GLU* 4.0 7.0 - - - +
443M THR 2.9 32.7 + - - +
444M PRO* 4.3 4.8 - - - +
445M GLU 4.8 0.4 - - - +
559M LEU* 2.8 36.9 + - + +
560M MET* 4.3 4.3 - - - +
562M SER* 1.3 74.4 - - - +
564M MET* 1.3 58.6 + - + +
566M THR* 3.2 24.9 - - - -
567M GLN* 3.7 13.5 + - - +
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Residues in contact with MET 564 (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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560M MET* 2.9 42.3 + - + +
561M GLY 4.4 0.9 - - - +
562M SER 3.2 0.2 + - - -
563M ASN* 1.3 75.2 - - + +
565M GLN* 1.3 61.8 + - - +
566M THR 3.0 1.8 - - - -
567M GLN* 2.9 38.3 + - - +
568M ALA 3.5 0.3 + - - -
838M LYS* 4.5 4.9 - - - -
840M ALA* 3.7 20.4 - - + -
841M ASN 4.6 3.6 - - - +
844M GLY* 4.2 11.7 - - - -
846M LYS* 3.6 35.2 - - + -
995M MET* 4.6 3.5 - - + +
997M LEU* 3.3 42.0 - - + +
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Residues in contact with GLN 565 (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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399M ASN* 3.5 12.0 + - - +
401M LEU* 4.0 9.2 - - + +
543M ASN* 2.9 35.0 - - - +
546M LEU* 3.5 25.3 - - - +
547M ILE* 3.9 8.0 - - - +
561M GLY 3.1 22.4 + - - +
562M SER* 3.2 7.0 + - - +
564M MET* 1.3 78.8 - - - +
566M THR* 1.3 61.5 + - - +
567M GLN 3.2 0.5 + - - -
568M ALA* 3.3 13.0 + - - +
668M LEU* 3.5 26.3 - - + +
842M ARG* 3.7 26.4 - - + +
995M MET* 4.1 22.2 - - + -
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Residues in contact with THR 566 (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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396M ASP* 3.4 24.5 - - - +
398M THR* 3.8 6.4 + - - -
399M ASN* 3.3 5.0 + - - +
401M LEU* 5.2 0.9 - - - -
402M SER* 3.1 42.8 + - - +
405M ARG* 3.4 33.9 + - - +
543M ASN* 3.3 20.0 + - - +
562M SER 3.8 0.5 + - - -
563M ASN 3.2 16.2 + - - -
565M GLN* 1.3 78.8 - - - +
567M GLN* 1.3 58.9 + - + +
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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