Contacts of the helix formed by residues 574 - 587 (chain D) in PDB entry 3IYD
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 VAL 574 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534D GLU* 4.5 6.5 - - - +
554D GLU* 3.6 23.8 - - + -
555D TYR* 3.4 40.6 - - + +
558D ASP* 5.3 2.0 - - - +
559D ALA 3.5 25.6 - - - +
560D ASN* 4.6 1.1 - - + -
563D LEU* 5.1 8.3 - - + -
573D THR* 1.3 83.9 + - - +
575D GLY* 1.3 60.6 + - - +
576D ARG 3.4 0.2 - - - -
577D ALA 3.8 2.2 - - - +
578D ILE* 3.2 31.4 + - + +
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Residues in contact with GLY 575 (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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513D MET* 3.2 26.5 - - - -
514D THR* 3.1 22.9 + - - +
573D THR* 3.1 7.5 - - - +
574D VAL* 1.3 82.7 - - - +
576D ARG* 1.3 58.9 + - - +
577D ALA 3.2 4.7 - - - -
578D ILE* 3.4 19.9 - - - +
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Residues in contact with ARG 576 (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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514D THR* 3.3 31.4 + - - +
516D ASP* 3.8 27.1 + - - +
536D LEU* 6.1 3.0 - - - +
572D THR* 3.6 30.5 + - + +
573D THR* 3.2 23.9 + - + +
575D GLY* 1.3 77.5 - - - +
577D ALA* 1.3 59.2 + - - +
578D ILE 3.8 0.7 - - - -
579D LEU 5.4 0.2 - - - -
580D TRP* 3.8 20.1 - - - +
593D ASN* 3.3 14.6 - - - +
594D GLN* 2.9 53.6 + - - +
595D ALA* 3.5 7.5 - - - +
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Residues in contact with ALA 577 (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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563D LEU* 3.7 30.8 - - + +
572D THR* 4.3 7.6 - - - +
573D THR 3.5 7.3 + - - +
574D VAL 3.8 4.0 - - - -
575D GLY 3.2 0.2 - - - -
576D ARG* 1.3 82.0 - - - +
578D ILE* 1.3 58.4 + - - +
579D LEU 3.5 1.3 - - - -
580D TRP* 4.1 21.5 - - + +
581D MET* 3.1 31.7 - - + +
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Residues in contact with ILE 578 (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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513D MET* 3.5 33.9 - - + -
514D THR* 4.9 0.7 - - - +
574D VAL* 3.2 14.8 + - + +
575D GLY* 3.4 22.9 - - - +
576D ARG 3.8 0.2 - - - -
577D ALA* 1.3 79.2 - - - +
579D LEU* 1.3 64.1 + - + +
581D MET* 3.7 28.6 - - + +
582D ILE* 3.8 11.3 - - - +
627D THR* 6.1 4.7 - - + -
631D TYR* 6.0 2.5 - - + +
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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
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510D LEU* 3.8 34.3 - - + -
513D MET* 5.5 1.1 - - - -
575D GLY 5.0 0.2 + - - -
576D ARG 5.4 0.4 - - - -
578D ILE* 1.3 85.1 - - + +
580D TRP* 1.3 61.3 + - - +
581D MET 3.1 7.0 + - - -
582D ILE* 3.1 34.4 - - + +
583D VAL* 3.5 8.8 - - + +
591D ILE* 5.7 6.3 - - + -
596D LEU* 4.2 28.5 - - + -
601D ILE* 5.9 1.6 - - + -
620D PHE* 3.4 30.7 - - + -
623D GLN 6.0 0.4 - - - +
624D ILE* 5.1 9.9 - - + +
627D THR* 5.6 1.3 - - - +
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Residues in contact with TRP 580 (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 ALA* 4.0 17.3 - - + -
566D LYS* 4.8 19.7 - - + +
570D LYS* 3.4 40.6 - - + -
572D THR* 5.9 4.7 - - + -
576D ARG 3.8 24.0 + - - +
577D ALA* 4.3 12.3 - - + -
578D ILE 4.1 1.4 - - - +
579D LEU* 1.3 79.0 - - + +
581D MET* 1.3 57.5 + - - +
582D ILE 3.6 0.2 - - - -
583D VAL* 4.5 8.5 - - + -
584D PRO* 3.5 16.0 - - + +
589D TYR* 4.9 4.8 + - - +
590D SER* 4.4 7.7 - - - +
591D ILE* 3.4 63.6 - - + +
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Residues in contact with MET 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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551D ARG* 4.7 27.1 - - + -
563D LEU* 6.2 0.4 - - - -
577D ALA* 3.1 23.1 + - + +
578D ILE* 3.7 39.3 - - + +
579D LEU 3.1 1.0 - - - -
580D TRP* 1.3 80.2 - - + +
582D ILE* 1.3 69.0 + - + +
583D VAL 3.3 2.2 - - - -
584D PRO* 3.1 20.2 - - - +
585D LYS* 4.2 5.0 + - - +
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Residues in contact with ILE 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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578D ILE 3.8 17.3 - - - +
579D LEU* 3.1 34.5 - - + +
581D MET* 1.3 89.2 - - + +
583D VAL* 1.3 61.4 + - - +
584D PRO 3.6 0.2 - - - -
585D LYS* 3.2 24.7 - - + +
586D GLY 4.2 1.4 + - - -
620D PHE* 4.2 19.6 - - + +
623D GLN* 3.9 37.9 - - + +
624D ILE 5.8 0.2 - - - +
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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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579D LEU* 3.5 20.4 - - + +
580D TRP* 4.5 9.4 - - + +
582D ILE* 1.3 74.8 - - - +
584D PRO* 1.3 68.9 - - + +
585D LYS 3.0 5.6 + - - -
586D GLY* 3.1 3.6 + - - -
587D LEU* 2.9 35.5 + - + +
589D TYR* 3.6 25.4 - - + +
591D ILE* 5.2 9.9 - - + -
604D MET* 5.2 5.6 - - + -
608D CYS* 4.8 7.4 - - - -
620D PHE* 3.5 29.6 - - + -
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Residues in contact with PRO 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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566D LYS* 3.3 33.0 - - - +
580D TRP* 3.5 14.8 - - + +
581D MET* 3.1 26.0 - - - +
583D VAL* 1.3 95.2 - - + +
585D LYS* 1.3 61.0 + - - +
586D GLY 3.2 5.9 + - - -
587D LEU 3.7 8.9 + - - +
588D PRO* 3.8 16.7 - - + +
589D TYR 5.6 0.4 - - - +
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Residues in contact with LYS 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 MET 4.2 2.9 + - - +
582D ILE* 3.2 25.1 - - + +
583D VAL 3.0 0.4 - - - -
584D PRO* 1.3 83.1 - - - +
586D GLY* 1.3 56.9 + - - +
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Residues in contact with GLY 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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582D ILE 4.2 1.0 + - - -
583D VAL 3.1 5.1 + - - -
584D PRO 3.9 2.8 - - - +
585D LYS* 1.3 81.3 - - - +
587D LEU* 1.3 74.1 + - - +
588D PRO* 4.1 3.6 - - - +
616D PRO* 5.7 6.3 - - - -
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Residues in contact with LEU 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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583D VAL* 2.9 22.3 + - + +
584D PRO* 3.9 0.7 - - - -
586D GLY* 1.3 87.2 - - - +
588D PRO* 1.3 68.0 - - + +
589D TYR* 2.9 52.9 - - + +
608D CYS* 4.6 9.4 - - + +
611D ILE* 4.7 1.3 - - + -
612D LEU* 3.6 51.1 - - + -
616D PRO* 4.0 20.4 - - + +
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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