Contacts of the helix formed by residues 548 - 560 (chain M) in PDB entry 6G0L
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 ASN 548 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519M LYS* 5.2 2.1 - - - +
545M LEU 4.4 9.6 - - - +
546M GLN 3.4 2.7 - - - -
547M ASN* 1.3 110.6 + - - +
549M ILE* 1.3 63.9 + - - +
550M LYS* 4.2 9.4 - - + +
551M GLU* 3.2 35.7 + - + +
552M LEU 4.0 3.1 + - - -
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Residues in contact with ILE 549 (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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545M LEU 5.9 0.4 - - - +
548M ASN* 1.3 70.5 - - - +
550M LYS* 1.3 75.1 + - + +
551M GLU 3.1 1.1 + - - -
552M LEU* 3.5 13.5 + - + +
553M ALA* 2.9 37.8 + - + +
574M ASN 5.8 7.9 - - - +
582M TYR* 3.4 41.3 - - + +
586M LEU* 4.2 12.1 - - + -
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Residues in contact with LYS 550 (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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519M LYS 4.1 8.4 - - - +
520M ASN* 5.6 6.5 - - - +
521M ALA* 5.4 14.3 + - - +
548M ASN* 3.2 7.8 - - + -
549M ILE* 1.3 90.4 - - + +
551M GLU* 1.3 50.0 + - + +
553M ALA* 4.4 8.9 - - + +
554M ALA* 2.7 38.4 + - - +
557M ASN* 6.0 2.6 - - - +
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Residues in contact with GLU 551 (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 HIS* 4.3 3.2 - - - -
518M LEU 5.0 0.6 - - - +
519M LYS* 3.3 48.2 - - + +
543M THR* 3.9 10.6 + - - +
544M PRO* 2.9 24.4 - - - +
545M LEU* 3.7 11.9 - - + -
547M ASN* 3.1 24.2 + - - +
548M ASN* 3.2 29.5 - - + +
549M ILE 3.1 0.6 - - - -
550M LYS* 1.3 75.2 - - + +
552M LEU* 1.3 61.5 + - - +
554M ALA* 3.2 4.0 + - - +
555M LEU* 2.9 33.7 + - + +
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Residues in contact with LEU 552 (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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398M ILE* 6.0 2.2 - - + -
545M LEU* 3.7 49.7 - - + +
546M GLN* 5.5 4.3 - - - +
548M ASN 4.0 2.9 + - - +
549M ILE* 3.5 14.0 + - + +
551M GLU* 1.3 79.5 - - - +
553M ALA* 1.3 58.7 + - - +
555M LEU* 3.1 6.2 + - + -
556M VAL* 2.9 43.9 + - + +
583M ILE* 5.8 3.8 - - + -
586M LEU* 3.8 33.7 - - + -
590M ILE* 4.7 20.4 - - + -
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Residues in contact with ALA 553 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549M ILE* 2.9 28.5 + - + +
550M LYS* 4.4 10.3 - - + +
552M LEU* 1.3 76.8 - - - +
554M ALA* 1.3 58.4 + - - +
556M VAL* 3.1 9.2 + - - +
557M ASN* 2.9 41.1 + - - +
564M PHE 5.1 13.1 - - - -
582M TYR* 6.0 0.2 - - - +
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Residues in contact with ALA 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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518M LEU 4.1 17.9 - - - +
519M LYS 4.7 2.7 - - - +
521M ALA* 4.6 13.0 - - + +
526M TYR* 2.7 31.3 + - + +
550M LYS 2.7 25.0 + - - +
551M GLU 3.2 5.8 + - - +
553M ALA* 1.3 77.3 - - - +
555M LEU* 1.3 57.1 + - - +
557M ASN* 2.8 13.5 - - - +
558M PHE* 2.8 13.6 + - - +
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Residues in contact with LEU 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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398M ILE* 3.8 35.4 - - + +
515M ALA 4.8 7.6 - - - +
518M LEU* 4.5 29.6 - - + +
539M LEU* 3.7 21.7 - - + +
541M THR* 5.2 4.3 - - + -
543M THR* 4.2 12.8 - - + -
545M LEU* 3.7 35.2 - - + -
551M GLU 2.9 16.0 + - - +
552M LEU* 3.7 8.1 - - + +
554M ALA* 1.3 77.1 - - - +
556M VAL* 1.3 63.6 + - - +
558M PHE* 4.0 7.3 + - + +
559M LEU* 4.1 11.8 + - - +
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Residues in contact with VAL 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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398M ILE* 6.4 0.7 - - + -
552M LEU* 2.9 30.1 + - + +
553M ALA* 3.1 9.2 + - - +
555M LEU* 1.3 78.4 - - - +
557M ASN* 1.3 59.9 + - - +
558M PHE 3.4 0.2 + - - -
559M LEU* 3.6 1.7 + - - +
560M MET* 2.9 30.5 + - + +
563M ARG* 3.7 34.3 - - + +
564M PHE 3.4 26.5 - - - +
586M LEU* 5.8 4.5 - - + -
590M ILE* 4.1 24.5 - - + -
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Residues in contact with ASN 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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521M ALA* 5.6 0.2 - - - +
526M TYR* 2.5 30.0 + - - -
550M LYS* 6.0 2.4 - - - +
553M ALA* 2.9 25.4 + - - +
554M ALA* 2.8 16.1 - - - +
556M VAL* 1.3 74.1 - - - +
558M PHE* 1.3 63.8 + - - +
559M LEU 3.3 0.2 - - - -
560M MET 3.4 13.9 - - - +
561M PRO* 3.7 24.7 - - + +
562M GLY 4.9 1.8 - - - +
563M ARG 4.6 11.9 + - - +
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Residues in contact with PHE 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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510M MET* 5.0 4.0 - - - -
518M LEU* 3.7 28.3 - - + -
526M TYR* 3.4 32.5 - + + +
529M LEU* 3.9 29.2 - - + -
530M ASN* 3.2 28.2 - - - +
537M ARG* 2.6 57.2 + - + -
539M LEU* 4.0 29.2 - - + -
554M ALA 2.8 23.6 + - - +
555M LEU* 4.1 6.1 - - + -
556M VAL 3.2 0.4 - - - -
557M ASN* 1.3 79.2 - - - +
559M LEU* 1.3 57.9 + - + +
561M PRO* 5.1 3.5 - - - +
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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
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396M ASN* 4.2 35.6 + - + +
398M ILE* 6.4 1.3 - - + -
537M ARG* 4.6 11.7 - - + +
539M LEU* 5.8 5.2 - - + -
555M LEU 4.1 9.7 + - - +
556M VAL 3.6 2.3 + - - +
558M PHE* 1.3 87.1 - - + +
560M MET* 1.3 71.7 + - + +
561M PRO* 3.6 8.6 - - - +
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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
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394M GLY 4.6 2.9 - - - +
395M ASP* 3.7 25.1 - - + +
396M ASN* 3.5 40.2 - - + +
556M VAL* 2.9 20.3 + - + +
557M ASN* 3.4 6.5 - - - -
559M LEU* 1.3 88.8 - - + +
561M PRO* 1.3 67.2 - - - +
562M GLY 3.1 3.5 + - - -
563M ARG* 3.5 41.6 + - + +
593M PHE* 5.6 4.3 - - + -
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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