Contacts of the helix formed by residues 612 - 627 (chain A) in PDB entry 3OPY
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 612 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A THR* 3.1 3.8 - - - +
611A SER* 1.3 77.6 + - - +
613A LEU* 1.3 62.1 + - - +
614A ASN 3.6 0.4 - - - -
615A PRO* 3.4 11.4 - - - +
616A ALA* 3.3 24.8 + - - +
695A ILE* 6.0 0.2 - - - -
739A LEU* 3.6 21.7 - - + +
740A GLY* 3.5 29.4 - - - +
871A PRO* 4.2 3.8 - - - +
875A ASP* 4.4 14.1 - - + +
879A ALA* 4.3 1.6 - - + +
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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
----------------------------------------------------------
605A HIS* 3.9 24.9 - - + +
608A ALA 4.6 2.2 - - - +
609A PRO* 4.2 1.3 - - + -
610A THR* 3.5 31.9 - - - +
611A SER 3.3 2.2 - - - -
612A ALA* 1.3 77.9 - - - +
614A ASN* 1.4 58.7 + - - +
616A ALA* 3.5 4.0 + - - +
617A THR* 2.8 31.9 + - - -
663A GLY 3.5 14.6 - - - +
664A SER* 4.2 4.0 - - - -
668A THR* 3.8 36.6 - - + +
695A ILE* 3.6 36.5 - - + +
696A GLY* 4.8 1.8 - - - +
726A ALA* 4.4 4.0 - - + -
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Residues in contact with ASN 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A HIS* 4.4 5.9 - - - -
611A SER 4.1 0.6 + - - -
613A LEU* 1.4 71.5 - - - +
615A PRO* 1.4 70.0 - - + +
617A THR* 3.1 4.4 + - - -
618A ARG* 2.9 23.4 + - - +
658A TRP* 3.4 34.8 - - + +
661A THR* 3.5 16.5 + - - +
662A GLY 3.6 11.9 + - - -
663A GLY 3.4 18.2 + - - -
664A SER* 3.8 2.8 - - - +
665A GLU* 3.2 51.3 + - - +
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Residues in contact with PRO 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A SER 3.4 12.8 - - - +
612A ALA* 3.4 19.1 - - - +
614A ASN* 1.4 89.1 - - + +
616A ALA* 1.3 58.4 + - - +
618A ARG* 3.3 6.0 + - + +
619A VAL* 3.2 27.8 + - + +
658A TRP 3.3 15.0 - - - +
659A HIS* 4.0 20.9 - - + +
661A THR 3.7 4.0 - - - +
871A PRO* 3.8 22.4 - - + -
876A ARG* 4.9 9.9 - - + +
879A ALA* 4.3 13.5 - - + -
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Residues in contact with ALA 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ALA 3.3 17.8 + - - +
613A LEU 3.7 4.0 - - - +
614A ASN 3.3 0.6 - - - -
615A PRO* 1.3 77.8 - - - +
617A THR* 1.4 57.9 + - - +
620A ALA* 3.1 25.4 + - - +
695A ILE* 4.6 11.2 - - + -
724A LEU* 4.5 11.7 - - + -
739A LEU* 4.1 14.4 - - + -
879A ALA* 3.8 26.1 - - + +
883A ALA* 3.3 12.2 - - - +
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Residues in contact with THR 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 4.0 22.4 - - + -
605A HIS* 2.7 34.5 + - + +
613A LEU 2.8 15.0 + - - -
614A ASN* 3.6 4.5 - - - -
616A ALA* 1.4 72.0 - - - +
618A ARG* 1.3 57.9 + - - +
620A ALA* 3.8 4.2 - - - +
621A THR* 2.7 41.5 + - - +
633A ALA* 5.9 0.2 - - + -
650A LEU* 4.7 5.8 - - + -
658A TRP* 3.6 24.2 - - + -
666A ILE* 5.5 4.7 - - + -
695A ILE* 3.3 9.4 - - - +
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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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416A ILE 5.5 2.8 + - - -
419A GLY* 4.0 24.2 - - - -
451A ARG* 4.4 11.1 - - - +
583A VAL* 5.0 8.3 - - - +
614A ASN 2.9 11.5 + - - +
615A PRO* 3.3 12.4 + - + +
617A THR* 1.3 74.7 - - - +
619A VAL* 1.4 76.6 - - - +
621A THR* 3.0 19.9 + - - -
622A LEU* 3.0 34.3 + - + +
655A VAL* 3.7 43.0 + - + +
657A ASP 5.6 0.6 - - - +
658A TRP* 4.0 9.8 - - + +
659A HIS* 3.5 45.9 + - - +
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Residues in contact with VAL 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A VAL* 4.4 11.4 - - + -
586A TYR* 4.5 1.1 - - + +
615A PRO* 3.2 15.2 + - + +
618A ARG* 1.4 92.1 - - - +
620A ALA* 1.3 57.6 + - - +
622A LEU* 3.5 9.9 + - + +
623A ASN* 2.9 29.9 + - - +
879A ALA* 6.0 0.2 - - + -
880A CYS* 3.6 50.7 - - + +
883A ALA* 3.9 11.9 - - + -
884A ILE* 3.8 19.1 - - + -
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Residues in contact with ALA 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 3.9 18.4 - - + -
616A ALA 3.1 18.4 + - - +
617A THR* 3.8 5.6 - - - +
619A VAL* 1.3 76.3 - - - +
621A THR* 1.4 57.4 + - - +
624A SER* 2.7 34.1 + - - -
693A ILE* 4.3 10.5 - - + -
695A ILE* 5.8 2.5 - - + -
724A LEU* 6.4 0.7 - - + -
883A ALA* 3.7 10.6 - - + +
887A CYS* 3.3 21.7 - - - -
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Residues in contact with THR 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 3.8 7.1 - - - +
617A THR* 2.7 24.5 + - - +
618A ARG 3.0 4.0 + - - -
620A ALA* 1.4 70.5 - - - +
622A LEU* 1.3 61.8 - - - +
624A SER* 3.4 1.9 + - - -
625A LEU* 2.9 52.0 + - + +
631A VAL* 3.7 15.7 - - + +
650A LEU* 3.6 43.8 - - + +
651A ASN 5.0 1.1 - - - +
655A VAL* 4.0 15.9 - - + +
658A TRP* 5.3 0.2 - - - -
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Residues in contact with LEU 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A VAL* 4.2 23.1 - - + -
586A TYR* 3.7 13.9 - - + -
618A ARG* 3.0 47.3 + - + +
619A VAL* 3.9 6.1 - - - +
621A THR* 1.3 72.7 - - - +
623A ASN* 1.4 65.5 + - - +
625A LEU* 4.6 2.7 - - + -
626A ALA* 2.9 27.5 + - - +
652A TRP* 3.7 36.8 - - + +
655A VAL* 3.5 29.4 - - + -
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Residues in contact with ASN 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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586A TYR* 2.7 38.2 + - - +
591A TYR* 5.9 1.3 - - - -
619A VAL 2.9 19.7 + - - +
620A ALA 3.8 4.5 - - - +
622A LEU* 1.4 76.9 - - - +
624A SER* 1.3 61.2 + - - +
626A ALA* 3.4 13.2 - - - +
627A LYS* 3.3 29.8 + - - +
884A ILE* 3.7 17.3 - - + +
887A CYS* 3.2 27.9 - - - +
888A ASN* 4.1 12.2 + - - +
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Residues in contact with SER 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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601A ILE* 4.5 7.8 - - - +
603A ILE* 5.8 0.5 - - - +
620A ALA 2.7 23.0 + - - -
623A ASN* 1.3 73.2 - - - +
625A LEU* 1.4 63.9 + - - +
627A LYS 3.2 10.4 + - - -
629A HIS* 3.2 29.8 + - - +
631A VAL* 3.6 21.0 - - - +
693A ILE* 5.5 0.2 - - - +
887A CYS* 3.5 6.1 - - - -
891A GLU* 2.6 33.2 + - - -
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Residues in contact with LEU 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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592A LEU* 4.9 1.6 - - - +
621A THR* 2.9 38.8 + - + +
622A LEU* 4.0 4.3 - - + +
624A SER* 1.4 69.1 - - - +
626A ALA* 1.4 59.3 + - - +
628A GLY* 3.0 19.8 + - - -
629A HIS 3.6 18.8 - - - +
630A ARG* 4.9 1.1 - - - -
631A VAL* 3.9 13.2 - - + +
649A GLU* 6.1 0.4 - - - +
650A LEU 3.7 15.9 - - - +
651A ASN* 3.6 12.1 - - - +
652A TRP* 3.5 59.3 + - + +
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Residues in contact with ALA 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A TYR* 3.7 36.5 - - + +
589A GLY* 4.9 3.6 - - - -
591A TYR* 3.4 18.0 + - + +
592A LEU* 3.1 25.3 + - - +
622A LEU 2.9 18.5 + - - +
623A ASN 3.4 8.3 - - - +
624A SER 3.3 0.2 - - - -
625A LEU* 1.4 74.6 - - - +
627A LYS* 1.3 57.2 + - - +
628A GLY 3.7 0.2 + - - -
652A TRP* 3.8 10.4 - - - -
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Residues in contact with LYS 627 (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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591A TYR* 3.4 31.6 - - + +
592A LEU* 3.8 4.3 - - - -
593A VAL* 3.1 39.0 + - + +
598A ARG* 3.7 1.9 + - - -
623A ASN* 3.3 32.6 + - - +
624A SER 3.2 0.4 + - - -
625A LEU 3.2 1.0 - - - -
626A ALA* 1.3 76.1 - - - +
628A GLY* 1.3 58.2 + - - +
629A HIS* 3.4 24.9 + - + +
887A CYS 3.8 11.5 + - - -
888A ASN* 3.8 14.8 + - - +
891A GLU* 2.7 36.2 + - - +
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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
------------------------------------------------------------
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