Contacts of the helix formed by residues 588 - 598 (chain A) in PDB entry 6C90
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLU* 3.7 11.2 - - - -
271A ILE* 3.9 5.6 - - - -
295A TRP* 3.5 3.0 + - - -
563A PHE* 3.7 27.2 - - - -
584A MET 3.0 12.9 + - - -
585A LEU 2.9 19.0 + - - -
586A GLU 4.4 0.5 - - - +
587A LYS* 1.3 81.9 - - - +
589A PHE* 1.3 62.1 + - - +
590A TYR* 3.7 6.1 + - - +
591A GLN* 3.1 17.7 + - - +
592A PHE* 3.1 17.5 + - - +
847A GLN* 4.1 2.6 + - - -
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Residues in contact with PHE 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TRP* 5.4 1.3 - + - -
267A GLU* 2.8 23.8 + - - +
288A ASN* 4.3 2.7 - - - -
291A GLN* 3.9 19.3 - - + -
292A PHE* 3.9 28.3 - + + -
295A TRP* 3.4 53.3 - + + +
559A LEU* 3.4 31.9 - - + -
560A ASN 4.7 0.2 - - - -
561A SER* 3.7 13.9 - - - -
588A SER* 1.3 69.4 - - - +
590A TYR* 1.3 61.0 + - - +
592A PHE* 4.1 6.7 - + + -
593A GLN* 2.8 61.0 + - + +
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Residues in contact with TYR 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLU* 3.9 0.2 + - - -
561A SER* 3.0 41.2 + - - +
563A PHE* 4.1 18.8 - - + -
588A SER* 3.2 7.2 - - - +
589A PHE* 1.3 77.5 - - - +
591A GLN* 1.3 60.6 + - - +
593A GLN* 3.5 6.5 + - + +
594A HIS* 3.3 19.2 + - - +
846A LEU* 3.6 31.1 - - + +
847A GLN* 3.8 36.1 - - + -
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Residues in contact with GLN 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A LEU 3.4 22.5 - - - +
586A GLU* 3.6 20.2 - - - +
588A SER* 3.1 11.7 + - - +
590A TYR* 1.3 76.3 - - + +
592A PHE* 1.3 65.4 + - - +
594A HIS* 3.3 12.4 + - - +
595A TYR* 3.1 53.8 + - + +
844A THR 3.2 21.0 + - - -
845A VAL* 3.4 11.6 - - - +
846A LEU* 2.9 33.9 + - - +
847A GLN* 5.3 1.8 - - - +
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Residues in contact with PHE 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO* 3.7 21.8 - - + -
99A VAL* 5.0 0.4 - - + -
291A GLN* 3.7 14.1 - - + -
294A GLU* 3.6 26.7 - - + -
295A TRP* 3.6 43.7 - + + -
298A HIS* 3.6 40.2 - + + -
586A GLU 5.2 0.8 + - - +
588A SER 3.1 7.3 + - - +
589A PHE* 3.1 11.4 + + + +
591A GLN* 1.3 77.9 - - - +
593A GLN* 1.3 62.5 + - - +
595A TYR* 3.2 11.0 + + + +
596A ARG* 3.0 50.6 + - + +
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Residues in contact with GLN 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ASN* 3.6 1.2 - - - +
291A GLN* 3.1 33.0 + - - +
559A LEU 3.2 14.3 + - - -
560A ASN* 3.1 25.6 + - - +
561A SER* 2.8 30.5 + - - -
589A PHE* 2.8 40.5 + - + +
590A TYR* 3.8 6.6 - - - +
591A GLN 3.3 0.2 - - - -
592A PHE* 1.3 75.0 - - - +
594A HIS* 1.3 57.7 + - - +
596A ARG* 3.4 0.9 + - - +
597A ALA* 2.8 32.6 + - - +
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Residues in contact with HIS 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A TYR 3.3 8.4 + - - +
591A GLN* 3.5 15.7 - - - +
592A PHE 3.2 0.8 - - - -
593A GLN* 1.3 74.9 - - - +
595A TYR* 1.3 75.0 + + - +
597A ALA* 4.5 4.0 - - - -
598A ILE* 3.0 38.7 + - + +
601A SER* 2.9 32.6 + - - -
844A THR* 3.1 29.8 + - - -
846A LEU* 3.9 32.8 - - + +
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Residues in contact with TYR 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ALA* 3.0 24.9 - - - +
95A LEU 4.9 2.0 + - - -
96A MET* 3.5 29.5 - - + +
97A PRO* 3.6 32.8 - - + -
298A HIS* 5.2 3.6 - - - -
586A GLU* 4.4 12.5 + - - +
591A GLN* 3.1 50.8 + - + +
592A PHE* 3.2 15.5 + + + +
594A HIS* 1.3 81.1 - + - +
596A ARG* 1.3 69.3 + - + +
598A ILE 3.4 18.3 - - - +
599A PRO* 3.8 6.6 - - - +
600A GLY 4.8 0.9 + - - -
601A SER 3.5 18.3 - - - +
843A ARG* 4.2 9.4 - - - -
844A THR 4.5 0.2 - - - -
845A VAL* 4.0 6.8 - - - +
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Residues in contact with ARG 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PRO* 4.5 20.2 + - - +
99A VAL* 3.8 32.1 + - - +
291A GLN* 3.5 27.1 - - + +
294A GLU* 2.8 35.8 + - - -
592A PHE* 3.0 44.1 + - + +
595A TYR* 1.3 83.6 + - + +
597A ALA* 1.3 66.2 + - - +
598A ILE 3.6 0.2 + - - -
599A PRO* 3.8 14.0 - - - +
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Residues in contact with ALA 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A GLN* 4.8 2.6 - - - +
593A GLN 2.8 20.0 + - - +
594A HIS* 4.0 4.3 - - - +
596A ARG* 1.3 77.5 - - - +
598A ILE* 1.3 74.2 + - + +
599A PRO* 3.4 7.7 - - - +
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Residues in contact with ILE 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A HIS* 3.0 28.9 + - + +
595A TYR 3.4 9.7 - - - +
597A ALA* 1.3 92.0 - - + +
599A PRO* 1.3 70.6 - - + +
600A GLY 3.3 0.2 + - - -
601A SER* 3.1 32.0 + - - +
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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