Contacts of the helix formed by residues 591 - 603 (chain M) in PDB entry 6C23
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 TRP 591 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C SER* 3.9 16.5 - - - -
115C PRO* 2.8 39.9 + - + +
116C LEU* 4.7 6.3 - - + -
120C PHE* 4.1 14.1 - + - -
680K LYS* 4.3 19.5 - - + -
232L VAL* 4.1 26.5 - - + -
295L HIS* 3.6 42.4 - + + -
296L PHE* 3.8 8.4 - + + -
589M PRO* 3.9 11.5 - - + +
590M GLU* 1.3 82.0 - - + +
592M LEU* 1.3 109.3 + - + +
593M ARG 3.2 2.5 - - - -
594M GLU* 3.1 5.6 + - - +
595M LYS* 2.9 40.2 + - + +
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Residues in contact with LEU 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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116C LEU* 5.6 6.5 - - + -
117C GLN 6.0 0.7 - - - +
118C GLN* 5.3 17.0 - - + +
120C PHE* 3.8 16.8 - - + -
295K PHE* 3.5 33.4 - - + -
589M PRO* 3.5 31.7 + - + +
591M TRP* 1.3 107.9 - - + +
593M ARG* 1.3 65.6 + - - +
595M LYS* 4.3 2.9 - - + -
596M THR* 2.9 24.9 + - - +
622M MET* 4.0 19.1 - - + -
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Residues in contact with ARG 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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588M ASP* 3.0 42.2 + - - +
589M PRO 3.7 2.4 + - - +
590M GLU* 3.6 39.8 + - - +
592M LEU* 1.3 75.9 - - - +
594M GLU* 1.3 73.5 + - + +
596M THR* 3.1 10.6 - - - +
597M ILE* 3.1 28.1 + - + +
619M LEU* 3.9 26.7 - - + -
622M MET* 4.1 5.7 - - - -
623M LYS* 4.9 9.8 - - - +
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Residues in contact with GLU 594 (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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269L ARG* 6.3 2.5 - - - +
296L PHE* 3.4 26.9 - - + -
590M GLU 4.1 14.1 - - - +
591M TRP 3.1 4.4 + - - +
593M ARG* 1.3 88.5 + - + +
595M LYS* 1.3 58.7 + - - +
597M ILE* 3.4 24.1 - - - +
598M THR* 2.9 38.6 + - + +
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Residues in contact with LYS 595 (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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120C PHE* 3.8 30.8 - - - -
295K PHE* 4.0 15.0 - - + -
680K LYS* 5.1 0.7 - - - +
232L VAL* 4.4 10.1 - - + -
233L GLU* 3.6 23.1 - - - +
296L PHE* 3.7 11.9 - - + -
591M TRP* 2.9 31.3 + - + +
592M LEU* 3.2 9.8 + - + +
594M GLU* 1.3 78.6 - - - +
596M THR* 1.3 58.9 + - - +
598M THR* 2.9 21.2 + - - +
599M GLN* 2.9 27.3 + - + +
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Residues in contact with THR 596 (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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292K TYR 4.5 7.4 + - - -
293K ASP* 4.4 7.6 + - - +
295K PHE* 3.7 24.6 - - - -
592M LEU 2.9 14.5 + - - +
593M ARG* 3.1 16.8 - - - +
595M LYS* 1.3 74.5 - - - +
597M ILE* 1.3 71.0 + - + +
599M GLN* 3.0 13.8 + - - +
600M ILE* 2.9 29.2 + - + +
615M LYS* 5.8 1.6 - - - +
618M ASN* 4.6 15.8 + - + -
619M LEU* 4.6 6.7 - - + -
622M MET* 3.9 19.0 - - + +
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Residues in contact with ILE 597 (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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593M ARG* 3.1 23.1 + - + +
594M GLU* 3.4 29.4 - - - +
596M THR* 1.3 78.9 - - + +
598M THR* 1.3 67.4 + - + +
600M ILE* 3.0 32.6 + - - +
601M GLU* 3.5 5.2 + - + +
615M LYS* 3.8 37.4 - - + +
619M LEU* 4.2 24.7 - - + -
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Residues in contact with THR 598 (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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296L PHE* 4.6 13.7 - - + -
594M GLU* 2.9 24.2 + - + +
595M LYS* 2.9 21.3 + - - +
597M ILE* 1.3 85.1 - - + +
599M GLN* 1.3 58.7 + - - +
601M GLU* 3.9 10.2 + - + +
602M GLU* 3.7 20.6 + - - +
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Residues in contact with GLN 599 (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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293K ASP* 3.1 32.7 + - - +
295K PHE* 3.1 40.0 - - - -
595M LYS* 2.9 23.5 + - + +
596M THR* 3.2 12.9 + - - +
598M THR* 1.3 74.3 - - - +
600M ILE* 1.3 65.6 + - - +
601M GLU 3.4 0.2 - - - -
602M GLU* 3.4 23.1 - - + +
603M PHE* 3.5 12.0 - - + -
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Residues in contact with ILE 600 (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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292K TYR 5.0 0.2 - - - +
293K ASP* 5.0 9.6 - - + +
596M THR* 2.9 22.4 + - + +
597M ILE* 3.0 7.8 + - - +
599M GLN* 1.3 76.7 - - - +
601M GLU* 1.3 63.6 + - - +
603M PHE* 3.0 41.9 + - + +
611M LYS* 3.5 43.0 - - + +
614M MET* 4.7 17.5 - - + -
615M LYS* 3.6 34.5 - - + -
618M ASN* 4.6 16.8 - - - +
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Residues in contact with GLU 601 (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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597M ILE* 3.5 7.3 + - + +
598M THR* 4.2 10.3 - - - +
599M GLN 3.4 0.6 - - - -
600M ILE* 1.3 75.2 - - - +
602M GLU* 1.3 61.9 + - - +
603M PHE 3.2 9.2 + - - +
611M LYS* 3.4 32.8 + - - +
615M LYS* 2.5 37.3 + - - +
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Residues in contact with GLU 602 (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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346L SER* 6.1 1.4 - - - -
598M THR 3.7 16.4 + - - +
599M GLN* 3.4 18.5 + - + +
601M GLU* 1.3 77.7 - - - +
603M PHE* 1.3 63.7 + - + +
604M SER* 3.7 2.8 + - - -
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Residues in contact with PHE 603 (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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284K LEU* 3.7 26.9 - - + -
293K ASP* 3.2 35.2 - - + -
599M GLN* 3.5 15.3 - - + -
600M ILE* 3.0 41.3 + - + +
601M GLU 3.2 9.2 - - - +
602M GLU* 1.3 83.0 - - + +
604M SER* 1.3 58.2 + - - +
605M ASP* 4.4 7.2 - - - +
606M VAL* 3.4 33.2 - - + +
611M LYS* 3.5 6.7 + - + -
614M MET* 6.3 1.6 - - - -
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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