Contacts of the helix formed by residues 588 - 593 (chain M) in PDB entry 6D6Q
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 SER 588 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267M GLU* 2.7 23.6 + - - -
271M ILE* 4.3 7.2 - - - -
295M TRP* 2.9 19.6 + - - -
563M PHE* 3.4 26.7 - - - -
584M MET 3.0 14.0 + - - -
585M LEU 3.5 11.3 + - - -
586M GLU 3.6 0.4 - - - +
587M LYS* 1.3 79.4 - - - +
589M PHE* 1.3 67.5 + - - +
590M TYR 3.4 7.3 + - - -
591M GLN* 4.1 3.4 - - - +
592M PHE* 3.4 16.5 + - - +
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Residues in contact with PHE 589 (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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257M MET* 5.4 7.9 - - + -
267M GLU* 3.2 20.6 + - + +
288M ASN* 4.2 10.8 - - - -
291M GLN* 4.7 12.3 - - + -
292M PHE* 4.4 30.7 - + + -
295M TRP* 3.9 32.2 - + + +
559M LEU* 3.2 30.5 - - + -
560M ASN 4.7 0.2 - - - -
561M SER* 3.5 14.1 - - - -
588M SER* 1.3 77.6 + - - +
590M TYR* 1.3 51.1 + - - -
591M GLN 3.0 4.9 - - - -
592M PHE* 4.3 5.6 - + - +
593M GLN* 2.7 79.6 + - + +
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Residues in contact with TYR 590 (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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561M SER* 4.2 15.4 - - - -
562M ALA 4.5 10.8 - - - -
563M PHE* 4.0 28.3 - + + -
588M SER* 3.4 2.4 + - - +
589M PHE* 1.3 76.7 - - - +
591M GLN* 1.3 54.2 + - + +
593M GLN* 4.5 7.9 - - - -
594M HIS* 2.3 57.4 + + - -
846M LEU* 3.8 34.2 - - + +
847M GLN* 3.8 27.4 - - + +
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Residues in contact with GLN 591 (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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585M LEU* 3.3 26.5 - - - +
586M GLU* 4.3 15.3 - - + +
588M SER* 3.9 5.8 + - - +
589M PHE 3.0 0.2 - - - -
590M TYR* 1.3 79.1 - - + +
592M PHE* 1.3 60.9 + - - +
593M GLN 3.0 3.8 - - - -
594M HIS* 2.7 27.5 + - - +
595M TYR* 3.0 47.1 + - + +
842M ALA 5.0 1.0 + - - -
844M THR 2.8 24.9 + - - +
845M VAL* 4.0 1.8 - - - -
846M LEU* 3.4 40.0 + - - +
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Residues in contact with PHE 592 (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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97M PRO* 3.8 38.1 - - + -
99M VAL* 5.0 3.6 - - + -
291M GLN* 3.0 49.7 - - + +
294M GLU* 3.4 38.8 - - + -
295M TRP* 3.4 40.6 - + + -
298M HIS* 4.8 7.2 - - + -
586M GLU 5.6 0.4 + - - -
588M SER 3.4 6.4 + - - +
589M PHE* 3.3 8.1 + + - +
591M GLN* 1.3 78.5 - - - +
593M GLN* 1.3 58.2 + - - +
594M HIS 3.2 1.0 + - - -
595M TYR* 3.5 19.8 + + + +
596M ARG* 4.9 2.6 + - - +
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Residues in contact with GLN 593 (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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288M ASN* 5.0 3.4 - - - +
291M GLN* 5.3 6.3 - - + -
558M PRO* 5.9 0.2 - - - +
559M LEU 3.9 2.2 + - - -
560M ASN* 2.2 37.9 + - - +
561M SER* 3.6 11.1 + - - +
589M PHE* 2.7 57.1 + - + +
590M TYR* 4.5 4.0 - - - -
591M GLN 3.0 0.2 - - - -
592M PHE* 1.3 73.4 - - - +
594M HIS* 1.3 70.5 + - + +
595M TYR 3.4 4.1 + - - -
596M ARG* 4.5 7.8 + - - +
597M ALA* 4.6 7.4 + - - +
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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