Contacts of the helix formed by residues 609 - 625 (chain A) in PDB entry 2YIC
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 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536A ALA* 3.9 17.9 - - + -
537A MET 4.7 9.6 - - - +
600A THR* 3.6 22.4 - - + -
601A ALA 3.6 23.6 - - - +
602A ASN* 3.8 22.4 - - + -
603A PRO* 5.0 0.4 - - - +
605A HIS 4.7 1.9 + - - +
607A GLU* 4.8 3.8 - - - +
608A ALA* 1.3 78.4 - - - +
610A ASP* 1.4 74.8 + - - +
611A PRO* 3.5 0.9 - - - -
612A VAL* 3.0 10.0 + - + -
613A LEU* 2.9 22.5 + - - +
991A PHE* 3.6 13.8 - - + -
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Residues in contact with ASP 610 (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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607A GLU* 2.5 56.8 + - - +
609A VAL* 1.4 84.4 - - - +
611A PRO* 1.4 65.6 - - + +
612A VAL 3.3 0.2 + - - -
613A LEU* 3.4 1.7 + - - +
614A GLU* 3.4 14.4 + - - +
641A MET* 3.4 44.9 - - + +
642A LEU 5.0 2.3 - - - +
643A HIS* 3.6 6.4 + - - -
653A VAL 5.0 0.7 - - - +
654A VAL* 3.7 11.8 - - - +
657A THR* 3.8 15.5 - - + +
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Residues in contact with PRO 611 (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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608A ALA 3.4 15.3 - - - +
610A ASP* 1.4 90.6 - - + +
612A VAL* 1.4 62.0 + - - +
614A GLU* 3.3 6.1 + - + +
615A GLY 3.1 18.7 + - - -
653A VAL* 3.7 14.1 - - + -
657A THR* 3.4 21.7 - - + +
660A LEU* 4.6 3.1 - - + -
953A PHE 4.2 2.0 - - - +
954A ALA* 3.2 43.5 - - + +
957A GLY* 4.0 12.3 - - - -
958A PHE* 3.3 10.5 - - - +
987A ILE* 4.4 1.3 - - + -
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Residues in contact with VAL 612 (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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600A THR* 4.6 11.9 - - - +
601A ALA 5.3 0.2 - - - +
608A ALA 4.0 5.8 - - - +
609A VAL* 3.0 15.1 + - + +
611A PRO* 1.4 74.2 - - - +
613A LEU* 1.4 65.0 + - - +
615A GLY 3.3 1.7 + - - -
616A LEU* 3.0 25.0 + - + +
957A GLY* 3.3 27.1 - - - +
960A TYR* 3.8 21.3 - - + -
961A GLY* 3.4 17.4 - - - -
964A VAL* 5.7 0.2 - - + -
987A ILE* 4.1 1.8 - - + -
991A PHE* 3.8 36.3 - - + -
1001A GLN* 5.2 2.2 - - - +
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Residues in contact with LEU 613 (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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534A VAL* 3.4 44.4 - - + +
535A ILE 4.1 7.2 - - - +
536A ALA* 3.6 24.5 - - + -
600A THR* 4.4 7.4 - - + -
609A VAL* 2.9 11.3 + - - +
610A ASP 3.6 8.3 - - - +
612A VAL* 1.4 76.8 - - - +
614A GLU* 1.3 62.7 + - - +
616A LEU* 3.3 6.1 + - + +
617A VAL* 2.9 26.4 + - + +
639A PRO* 3.8 21.3 - - + -
640A LEU 4.0 8.3 - - - +
641A MET* 3.8 30.1 - - + -
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Residues in contact with GLU 614 (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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610A ASP 3.4 11.9 + - - +
611A PRO* 3.3 9.7 + - + +
612A VAL 3.3 0.4 - - - -
613A LEU* 1.3 77.7 - - - +
615A GLY* 1.3 57.0 + - - +
617A VAL* 4.7 0.7 - - - -
618A ARG* 2.9 26.7 + - - +
639A PRO* 3.7 6.5 - - - +
641A MET* 3.1 21.0 - - - +
657A THR* 3.6 22.4 - - + +
660A LEU* 5.0 4.5 - - + -
661A ALA* 6.5 1.1 - - - -
666A TYR 5.0 1.4 - - - +
668A THR* 2.6 40.5 + - + +
671A THR* 2.6 25.0 + - - +
673A HIS* 5.1 0.5 - - - -
734A ASP* 5.4 0.3 - - - +
958A PHE* 3.5 17.7 - - + -
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Residues in contact with GLY 615 (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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611A PRO 3.1 11.3 + - - -
612A VAL 3.3 0.9 + - - -
614A GLU* 1.3 74.1 - - - +
616A LEU* 1.3 57.5 + - - +
618A ARG* 3.4 2.3 + - - +
619A ALA 2.9 24.9 + - - -
958A PHE* 3.3 41.4 - - - -
962A TYR* 3.3 17.8 - - - -
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Residues in contact with LEU 616 (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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534A VAL* 3.8 22.0 - - + -
598A SER* 5.4 0.2 - - - +
600A THR* 3.4 29.4 - - - +
612A VAL* 3.0 19.3 + - + +
613A LEU* 3.5 6.3 - - - +
615A GLY* 1.3 76.4 - - - +
617A VAL* 1.3 61.0 + - - +
619A ALA* 3.3 4.2 + - - +
620A LYS* 3.1 57.3 + - + +
961A GLY* 3.2 16.0 + - - +
964A VAL* 3.8 26.5 - - + -
965A GLY* 4.0 9.0 - - - -
1001A GLN* 5.4 0.2 - - - +
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Residues in contact with VAL 617 (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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534A VAL* 3.7 32.1 - - + -
613A LEU* 2.9 20.8 + - + +
614A GLU 3.8 3.1 - - - +
616A LEU* 1.3 75.3 - - - +
618A ARG* 1.3 58.3 + - - +
620A LYS* 3.1 4.7 + - - +
621A GLN* 2.8 38.7 + - - +
637A VAL* 3.4 34.8 - - + +
639A PRO* 3.8 35.7 - - + -
668A THR* 4.0 3.1 - - + -
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Residues in contact with ARG 618 (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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614A GLU 2.9 17.4 + - - +
615A GLY 3.6 2.5 - - - +
616A LEU 3.3 0.2 - - - -
617A VAL* 1.3 76.3 - - - +
619A ALA* 1.4 55.6 + - - +
621A GLN* 3.3 10.8 + - - +
622A ASP* 2.9 52.3 + - - +
628A GLU* 3.6 22.9 - - - +
629A GLU* 3.7 6.1 - - - +
664A ARG 2.9 29.3 + - - -
665A GLY 3.8 5.5 - - - -
666A TYR 3.4 3.6 - - - +
667A ARG 2.9 37.7 + - - +
668A THR* 3.8 7.2 - - + +
897A ARG* 4.5 2.6 - - - +
946A TYR* 3.2 27.9 + - - -
958A PHE* 3.5 25.6 - - + -
962A TYR* 4.0 11.9 - - + -
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Residues in contact with ALA 619 (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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615A GLY 2.9 15.5 + - - +
616A LEU 3.6 5.4 - - - +
617A VAL 3.3 0.2 - - - -
618A ARG* 1.4 74.1 - - - +
620A LYS* 1.4 58.2 + - - +
622A ASP* 3.4 3.5 + - - +
623A LEU* 3.0 33.9 + - - +
962A TYR* 3.2 51.9 + - + +
965A GLY 3.8 0.7 - - - -
966A ASN* 3.7 15.3 + - + +
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Residues in contact with LYS 620 (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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532A GLU* 2.8 41.6 + - - +
534A VAL* 3.9 8.7 - - + -
598A SER* 4.6 2.6 - - - -
616A LEU* 3.1 42.1 + - + +
617A VAL 3.1 7.8 + - - +
619A ALA* 1.4 72.7 - - - +
621A GLN* 1.4 58.4 + - - +
623A LEU* 3.3 12.1 + - + +
624A LEU* 3.1 32.9 + - + +
637A VAL* 4.0 15.9 - - + -
965A GLY* 4.2 14.8 + - - +
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Residues in contact with GLN 621 (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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617A VAL* 2.8 28.4 + - - +
618A ARG* 3.6 13.4 - - - +
620A LYS* 1.4 69.1 - - - +
622A ASP* 1.3 64.6 + - - +
624A LEU 3.2 1.6 + - - -
625A ASP 3.1 3.8 + - - -
626A THR* 3.0 53.5 + - + +
627A GLY* 4.6 1.3 - - - -
635A PHE* 3.6 24.2 - - - +
637A VAL* 2.9 34.5 + - + +
667A ARG 3.9 4.5 - - - +
668A THR* 2.7 43.6 + - - -
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Residues in contact with ASP 622 (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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618A ARG* 2.9 39.8 + - - +
619A ALA 3.4 2.9 + - - +
621A GLN* 1.3 75.2 - - - +
623A LEU* 1.4 63.4 + - - +
625A ASP* 3.2 13.7 + - - +
626A THR 4.6 3.2 - - - +
629A GLU* 3.5 31.0 + - + +
895A LEU* 4.8 12.3 - - + +
897A ARG* 5.0 0.5 + - - -
944A LEU* 3.5 12.2 - - + +
962A TYR* 2.6 39.0 + - - +
966A ASN* 6.1 0.2 - - - +
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Residues in contact with LEU 623 (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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619A ALA 3.0 15.4 + - - +
620A LYS* 3.5 13.0 - - + +
621A GLN 3.3 0.2 - - - -
622A ASP* 1.4 77.7 - - - +
624A LEU* 1.4 60.0 + - + +
625A ASP* 3.3 2.5 + - - +
895A LEU* 5.7 2.9 - - + -
965A GLY 4.0 11.9 - - - +
966A ASN* 3.5 45.8 - - + +
967A PRO* 5.8 0.9 - - + -
968A ASP* 6.2 0.2 - - + -
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Residues in contact with LEU 624 (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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531A ASP* 3.9 28.7 - - + +
532A GLU* 5.8 1.8 - - + +
620A LYS* 3.1 15.5 + - + +
621A GLN 3.2 4.2 + - - +
623A LEU* 1.4 75.8 - - + +
625A ASP* 1.3 70.8 + - - +
626A THR* 4.1 10.6 - - + -
632A ASP* 4.4 3.1 - - - +
636A SER* 4.1 2.7 - - - +
637A VAL* 3.6 31.0 - - + -
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Residues in contact with ASP 625 (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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621A GLN 3.1 2.8 + - - -
622A ASP 3.2 13.8 + - - +
623A LEU 3.3 2.8 - - - +
624A LEU* 1.3 80.9 - - - +
626A THR* 1.3 57.8 + - - +
629A GLU 3.8 6.2 - - - +
630A GLY* 3.3 12.6 - - - -
631A SER* 2.6 49.3 + - - -
632A ASP* 3.1 13.5 + - - +
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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