Contacts of the helix formed by residues 636 - 655 (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 636 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576A HIS* 6.2 0.2 - - - -
628A THR* 5.7 0.9 - - - -
631A SER* 5.3 4.3 - - - -
632A SER* 4.1 6.7 + - - +
633A GLN* 3.3 41.4 + - + +
634A PHE 3.0 6.1 + - - -
635A TYR* 1.4 80.9 - - - +
637A LYS* 1.3 68.6 + - - +
638A PHE* 3.6 25.6 - - - +
639A ASN* 3.2 24.6 + - - +
640A SER* 3.0 19.1 + - - -
733A GLN* 4.5 7.4 + - - +
736A SER* 5.2 2.3 + - - -
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Residues in contact with LYS 637 (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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625A VAL* 3.6 41.8 - - + +
626A GLU* 3.7 36.9 + - - +
628A THR* 4.1 18.3 - - + +
636A ASP* 1.3 78.3 + - - +
638A PHE* 1.3 95.7 + - + +
640A SER* 3.8 2.7 - - - -
641A ARG* 3.0 42.8 + - - +
683A ASP* 5.7 0.7 - - - -
686A PHE* 5.9 0.2 - - - -
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Residues in contact with PHE 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ASP* 3.0 21.0 - - - +
637A LYS* 1.3 113.1 - - + +
639A ASN* 1.3 61.0 + - - +
641A ARG* 4.3 1.6 - - - +
642A TYR* 3.0 27.0 + - - +
683A ASP* 3.7 22.0 - - - -
686A PHE* 3.7 35.4 - + - -
687A LEU* 4.0 9.0 - - + -
733A GLN* 5.1 12.3 - - - +
736A SER* 4.4 15.4 + - - +
740A LEU* 3.5 31.2 - - + +
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Residues in contact with ASN 639 (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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583A GLN* 5.7 4.3 - - - +
633A GLN* 3.7 6.9 - - - +
634A PHE* 3.3 31.1 - - + +
635A TYR* 4.0 10.8 - - + +
636A ASP* 3.2 28.0 + - - +
638A PHE* 1.3 72.3 - - - +
640A SER* 1.3 60.8 - - - +
642A TYR* 3.1 9.6 + - - +
643A SER* 2.8 33.5 + - - +
736A SER* 3.1 25.8 + - - -
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Residues in contact with SER 640 (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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579A GLY* 3.8 21.1 + - - -
582A VAL* 4.3 9.3 - - - +
621A PHE* 4.0 21.6 - - - -
625A VAL* 4.4 11.7 - - - +
635A TYR* 3.7 11.1 + - - +
636A ASP 3.0 17.1 + - - -
637A LYS 3.8 4.9 - - - -
639A ASN* 1.3 76.3 - - - +
641A ARG* 1.3 56.4 + - - +
643A SER* 3.2 2.8 + - - -
644A ILE* 2.8 36.4 + - - +
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Residues in contact with ARG 641 (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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622A TYR* 2.8 63.6 + - + +
623A VAL 3.7 1.2 + - - -
625A VAL* 3.8 9.3 - - + +
626A GLU* 2.9 50.1 + - - +
637A LYS* 3.0 41.3 + - - +
638A PHE* 3.4 3.9 + - - +
639A ASN 3.2 0.2 - - - -
640A SER* 1.3 77.7 - - - +
642A TYR* 1.3 54.0 + - - +
644A ILE* 3.3 2.5 + - - +
645A SER* 2.8 36.9 + - - -
679A ARG* 3.2 19.1 - - - +
683A ASP* 2.9 29.9 + - - -
740A LEU* 3.8 17.5 - - + -
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Residues in contact with TYR 642 (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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590A MET* 6.1 1.1 - - + -
638A PHE 3.0 14.5 + - - +
639A ASN* 3.3 12.6 - - - +
641A ARG* 1.3 73.8 - - - +
643A SER* 1.3 70.2 + - - +
645A SER* 3.1 13.2 + - - -
646A ILE* 3.2 36.8 + - + +
736A SER* 5.3 2.9 - - - +
739A GLY* 3.7 17.3 - - - -
740A LEU* 3.7 24.1 - - + +
743A LYS* 3.5 38.4 - - + -
796A SER* 4.8 8.0 + - - -
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Residues in contact with SER 643 (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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582A VAL* 3.8 21.5 - - - -
583A GLN* 3.9 16.3 + - - +
586A SER* 3.4 39.2 + - - -
639A ASN* 2.8 22.4 + - - +
640A SER* 3.7 4.3 - - - -
642A TYR* 1.3 79.4 - - - +
644A ILE* 1.3 61.5 + - - +
645A SER 3.4 0.2 + - - -
646A ILE* 3.4 9.2 + - - -
647A ILE* 3.4 8.6 - - - +
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Residues in contact with ILE 644 (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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582A VAL* 3.7 18.8 - - + -
618A LEU* 3.9 24.2 - - + +
621A PHE* 3.6 28.9 - - + -
622A TYR* 3.8 37.5 - - + +
625A VAL* 5.7 0.4 - - + -
640A SER* 2.8 25.6 + - - +
641A ARG* 3.7 5.4 - - + +
643A SER* 1.3 75.4 - - - +
645A SER* 1.3 58.9 + - - +
647A ILE* 3.2 10.2 + - - +
648A LEU* 2.9 48.2 + - + +
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Residues in contact with SER 645 (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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622A TYR* 3.9 10.9 + - - -
641A ARG 2.8 20.5 + - - -
642A TYR* 3.1 5.6 + - - -
644A ILE* 1.3 73.4 - - - +
646A ILE* 1.3 65.0 + - - +
648A LEU* 3.7 1.1 - - - +
649A GLU* 2.9 29.2 + - - +
740A LEU* 4.2 5.5 - - - +
743A LYS* 3.5 31.2 - - - +
744A SER* 4.9 1.4 + - - -
747A LEU* 3.5 27.3 - - - +
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Residues in contact with ILE 646 (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 SER* 4.1 16.6 - - - +
589A ALA* 4.6 6.5 - - + -
590A MET* 4.0 45.3 - - + +
591A PRO* 5.6 1.6 - - + -
642A TYR* 3.2 41.2 + - + +
643A SER* 3.7 7.6 - - - +
644A ILE 3.3 0.2 - - - -
645A SER* 1.3 76.3 - - - +
647A ILE* 1.3 62.4 + - - +
649A GLU* 3.4 8.6 + - - +
650A GLU* 3.1 28.6 + - + +
743A LYS* 3.9 22.4 - - - +
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Residues in contact with ILE 647 (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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582A VAL* 3.9 10.5 - - + +
585A LEU* 3.7 16.4 - - + +
586A SER* 3.6 33.0 - - - +
589A ALA* 4.0 12.1 - - + -
604A PHE* 4.4 15.5 - - + -
614A LEU* 4.6 4.7 - - + -
618A LEU* 3.5 38.4 - - + -
643A SER 3.4 17.5 - - - +
644A ILE* 3.2 5.3 + - - +
646A ILE* 1.3 71.5 - - - +
648A LEU* 1.3 66.6 + - - +
650A GLU* 4.1 0.2 - - - +
651A LEU* 2.8 45.1 + - + +
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Residues in contact with LEU 648 (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* 3.8 29.2 - - + -
618A LEU* 4.0 18.6 - - + -
619A LEU* 4.0 15.9 - - + -
622A TYR* 5.1 0.2 - - + -
644A ILE* 2.9 37.0 + - + +
645A SER* 3.7 4.5 - - - +
647A ILE* 1.3 76.9 - - - +
649A GLU* 1.3 63.1 + - - +
651A LEU* 3.8 4.1 - - + +
652A TYR* 3.2 24.1 + - - +
662A LEU* 5.7 0.6 - - + +
676A PHE* 3.9 28.5 - - + -
747A LEU* 4.0 15.7 - - + -
751A TYR* 3.8 18.1 + - - +
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Residues in contact with GLU 649 (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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645A SER 2.9 16.2 + - - +
646A ILE* 3.7 6.0 - - - +
648A LEU* 1.3 79.2 - - - +
650A GLU* 1.3 62.3 + - - +
652A TYR* 3.4 4.2 + - - +
653A TYR* 2.5 70.3 + - + +
743A LYS* 3.1 31.6 + - - +
746A LYS* 3.4 20.6 - - + +
747A LEU* 4.0 15.7 - - + +
750A ILE* 4.4 7.9 - - + -
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Residues in contact with GLU 650 (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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589A ALA* 3.4 27.0 - - + +
591A PRO* 3.3 27.4 - - + +
601A MET* 3.4 21.6 - - + +
646A ILE* 3.1 23.6 + - + +
647A ILE 4.1 1.8 - - - +
649A GLU* 1.3 79.4 - - + +
651A LEU* 1.3 69.1 + - - +
653A TYR* 3.7 20.5 - - - -
654A LYS* 2.7 56.7 + - - +
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Residues in contact with LEU 651 (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 MET* 4.3 5.2 - - + -
604A PHE* 3.9 29.8 - - + -
614A LEU* 4.1 4.0 - - + -
615A LEU* 4.5 11.0 - - + -
618A LEU* 3.9 15.0 - - + -
647A ILE* 2.8 46.7 + - + +
648A LEU* 3.8 4.5 - - - +
650A GLU* 1.3 71.5 - - - +
652A TYR* 1.3 57.8 + - - +
655A ILE* 2.8 44.9 + - + +
658A TYR* 3.8 54.1 - - + -
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Residues in contact with TYR 652 (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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648A LEU 3.2 15.7 + - - +
649A GLU 3.6 4.3 - - - +
650A GLU 3.2 0.2 - - - -
651A LEU* 1.3 77.8 - - - +
653A TYR* 1.3 66.4 + + - +
655A ILE 4.6 1.4 + - - -
656A PRO* 5.9 0.2 - - - +
658A TYR* 4.9 0.8 - - - +
659A LYS* 3.7 58.2 + - + +
662A LEU* 3.5 23.8 - - + +
663A ILE* 4.4 4.5 - - - +
750A ILE* 3.6 41.6 + - + -
751A TYR* 3.5 30.5 - + + -
754A ASP* 2.4 41.9 + - - +
755A ILE* 5.2 0.3 - - - +
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Residues in contact with TYR 653 (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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649A GLU* 2.5 61.0 + - + +
650A GLU* 3.3 22.2 + - - +
652A TYR* 1.3 81.3 - + - +
654A LYS* 1.3 79.2 + - + +
655A ILE 3.7 0.2 - - - -
656A PRO* 5.9 0.2 - - - +
746A LYS* 3.1 23.7 - - - +
750A ILE* 4.1 23.1 - - + +
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Residues in contact with LYS 654 (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 PRO* 4.5 7.1 - - - +
595A ASN 4.0 13.3 + - - -
596A SER 4.5 1.1 - - - -
597A PRO* 4.0 46.2 - - + -
601A MET* 4.0 14.1 - - + -
605A GLU* 5.0 2.6 - - - +
650A GLU* 2.7 39.8 + - - +
653A TYR* 1.3 93.9 - - + +
655A ILE* 1.3 64.7 + - + +
656A PRO* 3.7 9.0 - - - +
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Residues in contact with ILE 655 (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 MET* 3.6 50.7 - - + +
604A PHE* 4.3 4.7 - - + -
605A GLU* 3.8 43.1 - - + +
651A LEU* 2.8 18.2 + - + +
652A TYR 5.2 1.1 - - - -
653A TYR 3.7 1.0 - - - -
654A LYS* 1.3 84.4 - - + +
656A PRO* 1.4 66.6 - - + +
657A SER* 3.5 20.4 - - - +
658A TYR* 2.9 33.7 + - + -
659A LYS* 3.2 9.5 + - - +
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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