Contacts of the helix formed by residues 607 - 625 (chain A) in PDB entry 3M62
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 ASP 607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A GLY* 4.2 6.1 - - - +
560A GLU* 2.4 30.3 - - - +
603A ILE* 2.8 30.7 + - + +
606A HIS* 1.3 75.9 - - - +
608A GLU* 1.3 52.9 + - - +
609A LEU* 3.0 21.5 + - - +
610A VAL* 3.1 22.5 + - + +
611A ASN* 2.8 33.4 + - - +
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Residues in contact with GLU 608 (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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494A GLN* 4.3 10.8 - - + +
606A HIS 3.2 7.9 + - - +
607A ASP* 1.3 70.9 + - - +
609A LEU* 1.3 64.8 + - - +
611A ASN* 3.0 14.7 - - - +
612A LYS* 3.0 49.9 + - - +
962A 1PE 6.0 1.7 - - - +
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Residues in contact with LEU 609 (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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481A ILE* 4.9 4.3 - - + -
490A PHE* 4.6 6.7 - - + -
494A GLN* 3.7 23.2 + - - +
495A ILE* 3.7 39.7 - - + +
497A LEU* 3.6 19.5 - - + -
560A GLU* 3.9 37.0 - - + +
563A THR* 4.7 2.0 - - + +
564A MET* 5.3 2.5 - - + +
607A ASP* 3.0 9.4 + - - +
608A GLU* 1.3 77.5 - - - +
610A VAL* 1.3 62.1 + - - +
612A LYS* 4.9 3.1 - - + -
613A ASN* 2.9 46.1 + - - +
962A 1PE 6.2 0.7 - - - -
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Residues in contact with VAL 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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559A VAL* 4.0 13.5 - - + -
560A GLU* 4.0 16.2 - - - +
563A THR* 3.9 27.6 - - - +
603A ILE* 4.4 2.9 - - + +
604A PHE* 3.8 29.6 - - + -
607A ASP* 3.1 30.5 + - + +
609A LEU* 1.3 73.0 - - - +
611A ASN* 1.3 65.6 + - - +
612A LYS 3.1 2.2 - - - -
613A ASN 3.0 1.4 + - - -
614A LEU* 2.9 31.9 + - + +
658A TYR* 3.7 12.8 - - - +
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Residues in contact with ASN 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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604A PHE 3.6 13.9 - - - +
605A GLU 3.0 22.1 + - - +
606A HIS 4.0 3.8 + - - -
607A ASP 2.8 26.8 + - - -
608A GLU* 3.0 19.6 - - - +
610A VAL* 1.3 73.8 - - - +
612A LYS* 1.3 69.4 + - - +
613A ASN 3.6 0.3 + - - -
614A LEU 4.7 0.9 + - - -
615A LEU 5.4 0.2 + - - -
657A SER* 5.3 5.4 - - - +
658A TYR* 3.3 17.8 - - + +
661A GLN* 2.9 30.4 + - - +
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Residues in contact with LYS 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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494A GLN* 5.8 6.1 - - + +
496A LYS* 5.4 11.5 - - - +
567A ARG* 5.4 0.5 + - - -
608A GLU* 3.0 41.2 + - - +
609A LEU* 5.4 1.8 - - + -
611A ASN* 1.3 85.9 + - - +
613A ASN* 1.3 75.5 + - - +
616A TYR* 5.5 3.3 - - - +
661A GLN* 4.4 8.1 + - - +
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Residues in contact with ASN 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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497A LEU* 3.5 30.8 + - + +
563A THR* 4.0 12.6 - - + -
567A ARG* 3.4 35.3 + - + +
609A LEU* 2.9 43.1 + - - +
610A VAL 3.0 2.0 + - - -
612A LYS* 1.3 92.7 - - - +
614A LEU* 1.3 59.3 + - - +
615A LEU 3.5 2.2 - - - -
616A TYR* 3.7 3.4 + - - +
617A ALA* 3.0 27.9 + - - +
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Residues in contact with LEU 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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563A THR* 3.7 22.4 - - + +
566A LEU* 5.1 3.1 - - + -
585A LEU* 3.6 29.6 - - + -
604A PHE* 3.9 30.1 - - + -
610A VAL* 2.9 18.4 + - + +
611A ASN 4.7 0.6 - - - -
613A ASN* 1.3 73.5 - - - +
615A LEU* 1.3 61.2 + - - +
617A ALA* 3.2 4.1 + - + +
618A LEU* 2.8 49.0 + - + +
647A ILE* 4.6 2.5 - - + -
651A LEU* 4.1 11.7 - - + -
658A TYR* 3.7 24.9 - - + +
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Residues in contact with LEU 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 ASN 5.4 0.8 + - - +
612A LYS 5.7 0.2 - - - -
613A ASN 3.5 0.4 - - - -
614A LEU* 1.3 80.4 - - - +
616A TYR* 1.3 63.0 + - - +
618A LEU* 3.2 3.9 + - - -
619A LEU* 3.0 33.9 + - + +
648A LEU* 3.8 26.5 - - + -
651A LEU* 4.5 12.8 - - + -
658A TYR* 4.0 16.8 - - + +
661A GLN* 3.6 30.5 + - + +
662A LEU* 3.4 45.5 - - + +
665A GLN* 4.5 9.6 - - + -
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Residues in contact with TYR 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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502A ASP* 3.3 31.8 - - - +
567A ARG* 3.3 41.7 - - - +
612A LYS 5.5 2.2 - - - +
613A ASN* 3.7 9.9 + - - +
614A LEU 3.4 0.2 - - - -
615A LEU* 1.3 76.6 - - - +
617A ALA* 1.3 58.0 + - - +
619A LEU* 3.1 2.5 + - - -
620A ASP* 2.8 47.2 + - + +
665A GLN* 4.0 19.6 + - - +
669A ASN* 4.2 8.5 - - - -
672A PHE* 3.4 53.4 - + - +
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Residues in contact with ALA 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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563A THR* 4.4 3.6 - - + +
566A LEU* 3.7 22.7 - - + +
567A ARG* 3.7 30.3 - - + +
613A ASN 3.0 20.7 + - - +
614A LEU* 3.2 11.4 + - + +
616A TYR* 1.3 77.2 - - - +
618A LEU* 1.3 58.8 + - + +
620A ASP* 3.9 2.1 - - - +
621A PHE* 3.0 30.1 + - - +
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Residues in contact with LEU 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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566A LEU* 4.7 7.0 - - + -
582A VAL* 3.8 28.9 - - + -
585A LEU* 4.7 0.4 - - + -
614A LEU* 2.8 45.2 + - + +
615A LEU* 3.2 4.2 + - - +
617A ALA* 1.3 70.5 - - - +
619A LEU* 1.3 60.7 + - - +
621A PHE* 3.5 2.9 + - + -
622A TYR* 3.1 28.2 + - - +
644A ILE* 3.9 22.7 - - + +
647A ILE* 3.5 42.0 - - + -
648A LEU* 4.0 14.8 - - + -
651A LEU* 3.9 11.7 - - + -
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Residues in contact with LEU 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 LEU* 3.0 35.5 + - + +
618A LEU* 1.3 73.0 - - - +
620A ASP* 1.3 63.8 + - - +
622A TYR* 3.7 9.0 - - - +
623A VAL* 3.5 19.9 - - - +
648A LEU* 4.0 24.0 - - + -
662A LEU* 5.7 3.8 - - + -
665A GLN* 4.5 11.7 - - + -
672A PHE* 3.7 28.0 - - + -
673A PHE* 4.3 24.0 - - + -
675A ARG* 4.4 0.9 + - - -
676A PHE* 3.9 40.8 - - + +
751A TYR* 5.2 2.5 - - - +
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Residues in contact with ASP 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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566A LEU 5.3 3.7 - - - +
567A ARG* 5.2 2.8 + - - +
569A PRO* 4.7 12.3 - - - +
616A TYR* 2.8 30.9 + - + +
617A ALA* 3.9 4.5 - - - +
619A LEU* 1.3 78.0 - - - +
621A PHE* 1.3 61.1 + - - +
623A VAL* 3.2 5.5 + - - +
624A ILE* 3.1 42.0 + - - +
672A PHE* 3.6 16.2 - - + -
675A ARG* 2.6 31.8 + - - +
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Residues in contact with PHE 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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566A LEU* 4.5 17.4 + - + +
575A PRO* 4.6 7.2 - - + -
578A LYS* 3.7 59.0 - - + -
579A GLY* 4.2 2.5 - - - -
582A VAL* 4.3 14.4 - - + -
617A ALA 3.0 18.1 + - - +
618A LEU* 3.5 4.7 + - + +
620A ASP* 1.3 74.3 + - - +
622A TYR* 1.3 64.1 + - - +
623A VAL 3.1 1.0 + - - -
624A ILE* 4.3 21.8 - - + -
625A VAL* 3.2 50.0 + - + +
640A SER* 4.0 17.9 - - - -
644A ILE* 3.6 20.6 - - + -
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Residues in contact with TYR 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 LEU 3.1 17.2 + - - +
619A LEU 3.7 8.5 - - - +
620A ASP 3.2 0.2 - - - -
621A PHE* 1.3 76.2 - - - +
623A VAL* 1.3 57.9 + - + +
625A VAL* 3.4 4.4 - - - +
641A ARG* 2.8 83.5 + - + +
644A ILE* 3.8 29.8 - - + +
645A SER* 3.9 10.1 + - - -
648A LEU* 5.3 0.7 - - + -
676A PHE* 3.6 37.5 - + + -
679A ARG* 4.5 8.3 - - + -
680A MET* 3.4 41.8 - - + +
683A ASP* 5.0 2.3 + - - +
740A LEU* 4.3 2.1 - - - +
744A SER* 3.8 10.4 + - - -
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Residues in contact with VAL 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 LEU 3.5 15.7 - - - +
620A ASP 3.6 5.8 - - - +
621A PHE 3.1 0.2 - - - -
622A TYR* 1.3 76.9 - - + +
624A ILE* 1.3 68.6 + - + +
625A VAL 3.1 1.6 - - - -
626A GLU* 2.9 25.5 + - + +
641A ARG* 3.7 3.4 + - - +
675A ARG* 3.2 48.0 - - + +
676A PHE* 3.8 26.0 - - - +
679A ARG* 4.8 13.4 - - + -
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Residues in contact with ILE 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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566A LEU 6.0 2.2 - - - +
569A PRO* 4.3 23.8 - - + -
575A PRO* 6.6 0.2 - - + -
578A LYS* 6.1 4.5 - - - +
620A ASP* 3.3 41.5 - - - +
621A PHE* 3.9 22.4 - - + +
623A VAL* 1.3 81.2 - - + +
625A VAL* 1.3 65.0 + - + +
626A GLU 3.1 1.2 + - - -
627A LYS* 3.1 32.7 + - + +
675A ARG* 5.4 0.4 - - - +
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Residues in contact with VAL 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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575A PRO* 5.4 9.6 - - + +
621A PHE* 3.2 47.5 + - + +
622A TYR* 3.4 22.4 - - - +
623A VAL 3.0 1.0 + - - -
624A ILE* 1.3 79.5 - - + +
626A GLU* 1.3 62.7 + - - +
628A THR* 3.0 30.4 - - - +
635A TYR 5.8 1.6 - - - +
636A ASP 5.6 0.2 - - - +
637A LYS* 3.6 26.0 - - + +
640A SER* 4.4 12.3 - - - +
641A ARG* 3.8 14.4 - - + +
644A ILE* 5.7 0.4 - - + -
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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