Contacts of the helix formed by residues 580 - 591 (chain A) in PDB entry 1T9A
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 GLN 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A ALA* 3.7 21.1 - - + -
579A GLU* 1.3 70.7 - - - +
581A GLY* 1.3 63.9 + - - +
582A MET 3.4 2.5 - - - -
583A VAL* 3.0 17.6 + - + +
584A THR* 3.0 21.4 + - - +
597A HIS 3.5 8.7 + - - -
598A THR* 3.1 38.1 + - - +
599A HIS 4.1 0.6 - - - +
600A GLN* 3.7 8.6 + - - +
1698A P23 3.3 19.5 - - - -
113B TYR* 3.5 31.0 + - - +
114B PRO* 3.3 24.6 - - - +
135B LEU* 4.6 5.1 - - - +
1700B YF4 4.4 1.7 - - - -
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Residues in contact with GLY 581 (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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499A GLN* 3.0 27.2 + - - -
579A GLU* 3.2 8.3 + - - -
580A GLN* 1.3 71.6 - - - +
582A MET* 1.3 56.5 - - - +
584A THR* 2.9 11.1 + - - -
585A GLN* 2.8 31.2 + - - +
1698A P23 2.7 20.8 + - - -
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Residues in contact with MET 582 (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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355A HIS* 4.0 20.9 - - - +
498A GLY* 3.5 17.7 - - - -
499A GLN* 3.4 10.5 - - + +
502A MET* 3.4 33.2 - - + -
580A GLN 3.3 0.8 + - - -
581A GLY* 1.3 73.8 - - - +
583A VAL* 1.3 60.6 + - - +
585A GLN* 3.5 15.0 - - - +
586A TRP* 3.1 37.4 + - - -
651A VAL* 4.5 2.5 - - + -
695A 1TB 3.8 28.0 - - - +
701A FAD 3.9 9.2 - - + -
1698A P23 3.0 32.0 + - + +
1700B YF4 4.2 8.1 - - + -
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Residues in contact with VAL 583 (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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580A GLN* 3.0 17.5 + - + +
582A MET* 1.3 74.1 - - - +
584A THR* 1.3 66.0 + - - +
585A GLN 3.0 1.3 - - - -
586A TRP* 3.1 3.8 + - - +
587A GLN* 2.8 22.6 + - - +
598A THR* 3.4 27.6 - - + -
695A 1TB 3.7 17.0 - - + -
1698A P23 4.7 0.2 - - + -
114B PRO* 4.7 5.4 - - + -
115B GLY* 4.6 8.3 - - - +
119B LEU* 3.8 25.6 - - + -
1700B YF4 3.3 34.1 - - - +
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Residues in contact with THR 584 (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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499A GLN* 5.3 0.5 + - - -
579A GLU* 2.7 29.3 + - + +
580A GLN 3.0 14.5 + - - +
581A GLY* 2.9 19.6 + - - -
583A VAL* 1.3 75.6 - - - +
585A GLN* 1.3 52.1 + - - +
587A GLN* 3.1 9.0 + - - +
588A SER* 2.7 39.8 + - - -
595A TYR* 3.3 18.7 - - + -
598A THR* 3.4 28.9 - - - +
599A HIS* 4.0 12.3 - - - +
648A LYS* 4.0 6.3 - - - +
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Residues in contact with GLN 585 (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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355A HIS* 3.9 7.5 - - - -
499A GLN* 2.8 31.2 + - - +
581A GLY 2.8 16.9 + - - +
582A MET* 3.5 14.9 - - - +
584A THR* 1.3 77.4 + - - +
586A TRP* 1.3 60.2 + - + +
588A SER* 3.1 8.8 + - - -
589A LEU* 3.0 39.1 + - + +
650A PRO* 3.8 15.0 - - + +
651A VAL* 2.9 42.0 + - - +
652A LEU* 5.1 0.8 - - - +
654A MET* 3.5 23.6 - - - +
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Residues in contact with TRP 586 (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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354A MET* 3.9 13.9 - - + -
355A HIS* 5.3 0.2 + - - -
582A MET* 3.1 29.1 - - - +
583A VAL 3.1 7.8 + - - +
585A GLN* 1.3 82.1 - - + +
587A GLN* 1.3 58.2 + - - +
590A PHE* 2.8 64.7 + + - +
591A TYR* 3.7 4.3 - + - -
654A MET* 3.5 31.4 - - + +
656A ALA* 4.0 16.2 - - + -
657A GLY 5.2 1.6 - - - -
695A 1TB 3.2 87.3 + + + -
119B LEU* 3.9 18.2 - - + -
251B LYS* 4.3 7.6 - - - -
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Residues in contact with GLN 587 (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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583A VAL* 2.8 16.9 + - - +
584A THR* 3.5 11.1 - - - +
586A TRP* 1.3 77.2 - - - +
588A SER* 1.3 57.3 + - - +
591A TYR* 3.1 31.0 + - + +
593A HIS* 3.1 19.5 + - - -
594A ARG 3.6 17.0 - - - +
595A TYR* 3.3 21.9 - - + +
596A SER* 3.1 23.3 + - - +
598A THR* 2.9 42.6 + - - +
114B PRO* 5.4 0.3 - - - +
119B LEU* 4.2 18.8 - - + +
122B TYR* 5.0 2.3 - - - +
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Residues in contact with SER 588 (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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584A THR 2.7 24.9 + - - -
585A GLN* 3.4 8.8 - - - -
587A GLN* 1.3 76.6 - - - +
589A LEU* 1.3 65.4 + - - +
592A GLU* 4.2 3.1 + - - -
593A HIS* 3.6 41.7 + - - +
595A TYR* 2.6 24.2 + - - -
648A LYS* 4.5 5.7 - - - +
675A GLN* 5.2 0.7 - - - +
679A ARG* 5.1 0.3 - - - -
682A ARG* 5.0 0.2 + - - -
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Residues in contact with LEU 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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585A GLN* 3.0 32.2 + - + +
588A SER* 1.3 84.0 - - - +
590A PHE* 1.3 83.5 + - + +
592A GLU 4.9 1.3 + - - -
650A PRO* 5.8 6.1 - - + -
652A LEU* 6.2 2.0 - - + -
654A MET* 3.5 36.3 - - + -
665A ILE* 4.9 16.8 - - + -
675A GLN* 5.9 4.0 - - + +
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Residues in contact with PHE 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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586A TRP* 2.8 64.1 + + + +
589A LEU* 1.3 102.6 - - + +
591A TYR* 1.3 81.0 + - + +
592A GLU* 3.6 4.1 + - - +
594A ARG* 5.3 0.9 + - - -
654A MET* 4.6 1.8 - - + -
656A ALA* 4.2 21.8 - - + -
657A GLY* 5.6 3.1 - - - -
665A ILE* 6.2 3.1 - - + -
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Residues in contact with TYR 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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586A TRP* 3.7 13.5 - + - -
587A GLN* 3.1 26.9 + - + +
590A PHE* 1.3 95.8 - + + +
592A GLU* 1.3 70.4 + - - +
594A ARG* 2.9 37.3 + - - +
119B LEU* 3.8 40.5 - - + +
120B PRO* 3.8 20.0 - - + +
123B ASP* 3.4 43.7 - - + +
251B LYS* 4.0 11.7 + - - -
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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