Contacts of the helix formed by residues 580 - 591 (chain D) in PDB entry 1T9D
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C TYR* 3.5 27.0 - - - +
114C PRO* 2.8 44.6 - - - +
135C LEU* 5.5 0.4 - - - +
2703C PYD 4.2 0.7 - - - +
525D MET* 4.1 4.9 - - - +
551D ALA* 4.1 12.8 - - + -
579D GLU* 1.3 68.6 - - - +
581D GLY* 1.3 60.3 + - - +
582D MET 3.4 2.2 - - - -
583D VAL* 3.0 22.3 + - + +
584D THR* 2.8 28.6 + - - +
597D HIS 4.0 1.2 + - - -
598D THR* 3.0 30.4 + - - +
2702D P22 3.4 26.6 - - - +
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Residues in contact with GLY 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D GLN* 3.1 32.8 + - - -
579D GLU* 3.0 9.0 + - - -
580D GLN* 1.3 71.7 - - - +
582D MET* 1.3 56.8 + - - +
584D THR* 3.0 9.2 + - - -
585D GLN* 2.9 24.6 + - - +
2702D P22 2.8 23.3 + - - -
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Residues in contact with MET 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2695C 1MM 3.9 30.3 - - + +
355D HIS* 4.0 21.3 - - - +
498D GLY* 3.6 30.5 - - - +
499D GLN* 3.7 14.4 - - + +
502D MET* 3.5 31.6 - - + -
580D GLN 3.4 0.8 - - - -
581D GLY* 1.3 73.6 - - - +
583D VAL* 1.3 62.0 + - + +
585D GLN* 3.5 11.8 + - - +
586D TRP* 3.3 35.7 + - - -
651D VAL* 4.2 3.6 - - + -
2702D P22 2.9 16.0 + - + +
3701D FAD 4.1 11.2 - - + -
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Residues in contact with VAL 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PRO* 4.8 5.6 - - + -
115C GLY* 4.6 6.1 - - - +
119C LEU* 3.7 28.0 - - + -
2695C 1MM 3.8 17.7 - - + -
2703C PYD 4.5 14.8 - - + -
580D GLN* 3.0 30.8 + - + +
582D MET* 1.3 75.4 - - + +
584D THR* 1.3 66.6 + - - +
585D GLN 3.1 1.6 - - - -
586D TRP* 3.1 4.0 + - - +
587D GLN* 2.9 21.7 + - - +
598D THR* 3.3 26.2 - - + -
2702D P22 5.0 4.5 - - + -
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Residues in contact with THR 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D GLN* 5.1 0.2 + - - -
579D GLU* 2.7 29.3 + - + +
580D GLN 2.8 19.7 + - - +
581D GLY* 3.0 12.8 + - - -
583D VAL* 1.3 75.5 - - - +
585D GLN* 1.3 57.7 + - - +
587D GLN* 3.2 8.9 + - - +
588D SER* 2.9 34.1 + - - -
595D TYR* 3.5 10.7 - - + -
598D THR* 3.4 31.9 - - - +
599D HIS* 4.1 11.9 - - + +
648D LYS* 4.0 9.3 - - - +
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Residues in contact with GLN 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D HIS* 4.0 5.1 - - - -
499D GLN* 2.7 30.5 + - - +
581D GLY 2.9 17.4 + - - +
582D MET* 3.5 13.1 - - - +
583D VAL 3.1 0.2 - - - -
584D THR* 1.3 79.3 + - - +
586D TRP* 1.3 60.1 + - + +
588D SER* 3.3 7.0 + - - -
589D LEU* 3.0 30.1 + - + +
650D PRO* 3.7 16.8 - - + +
651D VAL* 2.7 42.8 + - - +
652D LEU* 5.1 0.8 - - - +
654D MET* 3.5 28.4 - - + +
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Residues in contact with TRP 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LEU* 3.9 20.2 - - + -
251C LYS* 6.0 4.9 - - - -
2695C 1MM 3.3 81.4 + + + -
354D MET* 4.1 8.5 - - + -
582D MET* 3.3 19.9 - - - +
583D VAL 3.1 8.3 + - - +
585D GLN* 1.3 79.4 - - + +
587D GLN* 1.3 59.2 + - - +
589D LEU* 4.5 0.9 - - - -
590D PHE* 2.7 67.6 + + + +
591D TYR* 3.8 4.4 - + + -
654D MET* 3.4 33.0 - - + +
656D ALA* 4.1 18.8 - - + -
657D GLY 5.2 2.9 - - - -
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Residues in contact with GLN 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PRO* 5.5 0.4 - - - +
119C LEU* 3.9 25.0 - - + +
122C TYR* 5.2 1.6 - - - +
123C ASP* 6.1 0.4 - - - +
583D VAL* 2.9 16.6 + - - +
584D THR* 3.2 7.3 + - - +
586D TRP* 1.3 75.8 - - - +
588D SER* 1.3 57.2 + - - +
591D TYR* 2.9 45.2 + - + -
593D HIS* 3.1 5.6 + - - -
594D ARG 3.6 16.2 + - - +
595D TYR* 3.2 20.1 - - + -
596D SER* 3.2 35.5 + - - +
598D THR* 2.8 35.1 + - - +
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Residues in contact with SER 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584D THR 2.9 22.8 + - - -
585D GLN* 3.6 8.1 - - - -
587D GLN* 1.3 78.4 - - - +
589D LEU* 1.3 60.7 + - - +
592D GLU* 4.2 3.6 + - - -
593D HIS* 3.6 40.6 + - - +
595D TYR* 2.5 25.8 + - - -
648D LYS* 4.5 4.7 - - - +
675D GLN* 4.7 5.3 - - - +
679D ARG* 5.0 0.3 - - - -
682D ARG* 5.2 0.2 + - - -
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Residues in contact with LEU 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585D GLN* 3.0 18.9 + - + +
588D SER* 1.3 80.0 - - - +
590D PHE* 1.3 90.3 + - + +
592D GLU 5.1 0.6 + - - -
652D LEU* 6.4 0.7 - - + -
654D MET* 3.5 32.8 - - + -
665D ILE* 4.1 23.6 - - + -
675D GLN* 5.9 0.2 - - - -
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Residues in contact with PHE 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D TRP* 2.7 65.5 + + - +
589D LEU* 1.3 107.6 - - + +
591D TYR* 1.3 79.8 + - + +
592D GLU* 3.6 4.8 + - - +
654D MET* 4.6 1.3 - - + -
656D ALA* 4.1 23.6 - - + -
657D GLY* 5.3 5.2 - - - -
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Residues in contact with TYR 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LEU* 3.8 30.3 - - + +
120C PRO* 3.5 30.6 - - + +
123C ASP* 3.3 44.0 - - + +
251C LYS* 4.6 8.5 - - - -
255C ALA* 5.7 0.7 - - - +
586D TRP* 3.8 13.0 - + - -
587D GLN* 2.9 30.0 + - + +
590D PHE* 1.3 98.3 - + + +
592D GLU* 1.3 60.0 + - - +
594D ARG* 2.6 40.2 + - - +
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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