Contacts of the helix formed by residues 577 - 595 (chain D) in PDB entry 2R17
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 ALA 577 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D GOL 3.0 11.5 + - - +
575D GLU 5.4 0.2 - - - +
576D LEU* 1.3 78.1 - - - +
578D GLU* 1.3 63.6 + - + +
580D PRO* 3.1 7.6 - - - +
581D LEU* 2.9 32.0 + - - +
613D LEU* 3.9 9.2 - - + +
617D GLU* 3.4 38.8 - - + +
618D ILE* 4.1 9.9 - - + -
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Residues in contact with GLU 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D GOL 2.8 32.4 + - - +
577D ALA* 1.3 72.5 - - - +
579D LEU* 1.3 61.1 + - - +
581D LEU* 3.5 7.1 + - - +
582D ARG* 2.5 65.8 + - - +
618D ILE* 3.9 21.4 - - + +
623D ALA* 3.3 29.4 - - - +
627D ALA* 4.5 8.1 - - - +
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Residues in contact with LEU 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B HIS* 4.8 10.5 - - + +
63B PHE* 4.0 21.8 - - + -
1D GOL 2.8 18.7 + - - +
526D ARG* 3.9 15.0 - - + +
530D PRO* 3.7 27.8 - - + -
571D LEU* 4.8 4.0 - - + -
576D LEU* 4.5 13.2 - - + -
578D GLU* 1.3 70.1 - - - +
580D PRO* 1.3 73.3 - - + +
582D ARG* 3.0 8.6 + - - +
583D LEU* 2.8 41.4 + - + +
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Residues in contact with PRO 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568D ILE* 3.7 13.8 - - + +
571D LEU* 3.7 25.4 - - + -
572D ILE* 3.8 14.6 - - + -
576D LEU* 3.8 18.8 - - + +
577D ALA 3.1 20.9 - - - +
579D LEU* 1.3 97.0 - - + +
581D LEU* 1.3 56.7 + - - +
583D LEU* 3.1 7.5 + - + +
584D PHE* 2.9 33.7 + - - -
613D LEU* 3.8 14.8 - - + -
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Residues in contact with LEU 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D ALA 2.9 17.3 + - - +
578D GLU* 3.6 7.2 - - - +
580D PRO* 1.3 74.4 - - - +
582D ARG* 1.3 68.0 + - + +
584D PHE* 3.2 6.4 + - - +
585D LEU* 3.1 30.7 + - + +
610D ALA* 3.2 38.1 - - + +
613D LEU* 3.5 15.6 - - + +
614D TYR* 4.4 18.2 - - + +
618D ILE* 4.5 11.7 - - + -
627D ALA* 3.8 28.9 - - + -
630D LEU* 6.2 1.1 - - + -
631D ILE* 4.2 12.8 - - + -
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Residues in contact with ARG 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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62B ASP* 3.1 30.8 + - - +
63B PHE* 3.8 26.1 - - + +
88B HIS* 6.0 1.0 + - - -
578D GLU* 2.5 53.2 + - - +
579D LEU* 3.0 11.1 + - - +
581D LEU* 1.3 84.3 - - + +
583D LEU* 1.3 61.1 + - - +
585D LEU* 3.4 8.2 + - + +
586D GLN* 3.2 26.0 + - - +
626D ALA* 5.2 12.5 - - - +
627D ALA* 4.6 13.3 - - - +
630D LEU* 3.4 38.1 - - + +
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Residues in contact with LEU 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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63B PHE* 4.1 8.3 - - + -
530D PRO* 4.5 9.6 - - + +
533D VAL* 4.1 26.5 - - + -
534D PHE* 3.8 35.0 - - + -
537D TYR* 3.0 19.8 + - + -
568D ILE* 3.5 17.5 - - + -
571D LEU* 3.5 32.5 - - + -
579D LEU* 2.8 33.8 + - + +
580D PRO* 3.1 6.3 + - + +
582D ARG* 1.3 73.2 - - - +
584D PHE* 1.3 63.3 + - - +
586D GLN* 3.2 5.5 + - - +
587D GLY 3.0 7.4 + - - -
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Residues in contact with PHE 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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565D HIS* 4.0 31.6 - + - -
568D ILE* 3.4 40.4 - - + -
569D SER* 4.4 6.1 - - - -
572D ILE* 3.8 17.0 - - + -
580D PRO 2.9 19.2 + - - -
581D LEU 3.6 7.4 - - - +
583D LEU* 1.3 74.3 - - - +
585D LEU* 1.3 59.5 + - - +
587D GLY* 3.1 1.4 + - - -
588D ALA* 2.8 24.9 + - - +
606D PHE* 3.4 42.3 - + - +
609D GLN* 3.1 40.2 - - + -
610D ALA* 3.9 4.5 - - + -
613D LEU* 4.1 11.9 - - + -
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Residues in contact with LEU 585 (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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581D LEU* 3.1 25.0 + - + +
582D ARG* 3.7 8.1 - - + +
583D LEU 3.3 0.2 - - - -
584D PHE* 1.3 75.4 - - - +
586D GLN* 1.3 59.5 + - + +
588D ALA* 3.0 8.9 + - - +
589D LEU* 2.9 28.9 + - - +
607D MSE 4.0 23.6 - - + -
610D ALA* 3.7 19.7 - - + -
630D LEU* 4.3 20.2 - - + -
631D ILE* 4.1 36.3 - - + +
634D THR* 3.8 30.5 - - + +
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Residues in contact with GLN 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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14B ARG* 3.7 24.7 + - - +
62B ASP* 4.6 4.8 + - - -
63B PHE* 3.9 17.1 - - + -
93B TRP* 5.9 3.2 - - - -
115B HIS* 5.7 5.9 - - - -
139B TYR* 4.4 11.1 - - - -
141B ALA* 4.4 12.1 + - - +
534D PHE* 3.9 17.6 - - + -
537D TYR* 3.7 17.0 - - + -
582D ARG 3.2 14.8 + - - +
583D LEU* 3.4 10.5 - - - +
584D PHE 3.2 0.2 - - - -
585D LEU* 1.3 79.6 - - - +
587D GLY* 1.3 57.9 + - - +
589D LEU* 3.3 17.8 + - - +
590D ALA* 2.9 28.6 + - - +
634D THR* 5.9 1.0 + - - -
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Residues in contact with GLY 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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537D TYR* 3.3 29.1 + - - -
561D PHE* 3.8 1.4 - - - -
583D LEU 3.0 10.9 + - - -
584D PHE 3.1 3.5 + - - -
586D GLN* 1.3 73.4 - - - +
588D ALA* 1.3 58.9 + - - +
590D ALA* 3.7 1.3 - - - +
591D ALA* 2.7 38.2 + - - +
606D PHE* 3.6 15.0 - - - -
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Residues in contact with ALA 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584D PHE 2.8 13.5 + - - +
585D LEU 3.0 10.1 + - - +
587D GLY* 1.3 75.6 - - - +
589D LEU* 1.3 62.8 + - - +
591D ALA* 3.8 1.2 - - - +
592D GLY* 3.0 20.8 + - - -
603D ALA* 3.9 16.7 - - - +
606D PHE* 3.8 10.0 - - + +
607D MSE 3.5 41.1 - - + +
634D THR* 5.0 0.2 - - + -
638D MSE 3.9 10.2 - - - +
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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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93B TRP* 3.9 26.2 - - + -
140B ASN* 6.1 0.2 - - - +
141B ALA* 4.0 19.1 - - + -
142B LEU* 4.5 18.6 - - + -
585D LEU 2.9 7.7 + - - +
586D GLN* 3.3 24.9 - - - +
588D ALA* 1.3 73.9 - - - +
590D ALA* 1.3 66.2 + - - +
592D GLY* 3.3 3.1 + - - -
593D GLU* 3.0 26.9 + - - +
634D THR* 3.1 48.5 - - + +
637D ARG* 5.0 2.2 - - + -
638D MSE 3.9 14.6 - - + +
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Residues in contact with ALA 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 3.8 19.1 - - - +
141B ALA* 4.0 8.9 - - - +
537D TYR* 4.4 8.5 - - + -
541D PHE* 4.1 9.9 - - + -
561D PHE* 4.0 16.8 - - + -
586D GLN 2.9 17.2 + - - +
587D GLY* 3.7 4.5 - - - +
589D LEU* 1.3 75.0 - - - +
591D ALA* 1.3 66.4 + - - +
593D GLU* 3.0 14.8 + - - +
594D ILE* 3.1 16.5 + - - +
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Residues in contact with ALA 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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561D PHE* 3.6 20.3 - - + -
587D GLY 2.7 21.9 + - - +
588D ALA 3.8 3.1 - - - +
590D ALA* 1.3 74.9 - - - +
592D GLY* 1.3 62.7 + - - +
593D GLU 3.0 1.4 + - - -
594D ILE* 3.2 9.4 + - - +
595D GLY 3.7 3.6 + - - -
596D PHE* 4.2 6.1 - - + -
599D HIS* 3.4 21.1 + - - +
602D VAL* 4.2 10.5 - - + -
603D ALA* 4.1 23.1 - - - +
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Residues in contact with GLY 592 (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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588D ALA 3.0 11.7 + - - -
589D LEU* 3.7 3.6 - - - -
591D ALA* 1.3 78.8 - - - +
593D GLU* 1.3 62.4 + - - +
594D ILE 3.5 0.4 - - - -
595D GLY 4.8 0.2 + - - -
599D HIS* 3.9 11.6 - - - -
603D ALA* 4.2 1.5 - - - +
638D MSE 6.0 2.2 - - - -
640D CYS* 3.6 39.5 - - - +
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Residues in contact with GLU 593 (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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141B ALA 3.1 23.8 - - - +
142B LEU* 3.6 34.0 - - + +
541D PHE* 4.0 13.5 - - + -
544D LYS* 3.6 10.2 + - - -
589D LEU 3.0 15.4 + - - +
590D ALA 3.0 7.0 + - - +
592D GLY* 1.3 82.1 - - - +
594D ILE* 1.3 64.0 + - - +
637D ARG 5.3 2.8 - - - +
638D MSE 6.0 1.6 - - - -
639D LYS* 5.6 9.6 - - - +
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Residues in contact with ILE 594 (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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540D ALA* 3.4 42.6 - - + +
541D PHE* 3.7 27.1 - - + +
544D LYS* 3.2 37.7 + - + +
553D TRP* 3.7 29.7 - - + -
557D CYS* 4.2 2.9 - - - -
561D PHE* 4.3 10.1 - - + -
590D ALA 3.1 15.3 + - - +
591D ALA 3.2 2.9 + - - +
592D GLY 5.0 0.2 - - - -
593D GLU* 1.3 79.6 - - - +
595D GLY* 1.3 62.2 + - - +
596D PHE* 4.0 12.8 - - + -
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Residues in contact with GLY 595 (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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553D TRP* 4.6 5.1 - - - -
554D GLU* 3.8 7.1 - - - +
591D ALA 3.7 7.9 + - - -
592D GLY 5.4 0.2 - - - -
593D GLU 3.9 0.2 - - - -
594D ILE* 1.3 80.3 - - - +
596D PHE* 1.3 68.4 + - - +
599D HIS* 3.6 26.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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