Contacts of the helix formed by residues 610 - 628 (chain A) in PDB entry 2W3C
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 610 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A GLN* 3.2 27.4 + - - +
438A TRP* 3.9 7.9 - - + -
442A VAL* 3.9 27.5 - - + +
446A HIS* 3.0 24.0 + - - -
449A GLN* 4.8 0.7 - - - +
496A MET* 4.0 11.9 - - + -
593A ALA* 5.0 0.2 - - - -
597A PRO 5.7 0.9 - - - +
599A PRO* 6.1 0.2 - - - +
601A PHE* 5.3 0.9 - - - -
609A PHE* 1.3 73.8 - - - +
611A HIS* 1.3 72.6 + - - +
612A GLU* 3.4 15.7 + - - +
613A PHE* 2.9 23.0 + - + +
614A THR* 3.2 13.8 + - - +
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Residues in contact with HIS 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 5.6 0.4 + - - -
593A ALA* 3.1 27.0 + - - +
594A SER* 3.3 24.3 + - - -
595A GLN 3.9 3.6 - - - -
596A LYS* 2.9 34.6 + - - +
597A PRO* 3.8 28.8 - - + +
609A PHE 4.2 1.2 + - - -
610A ASP* 1.3 74.4 + - - +
612A GLU* 1.3 74.0 + - + +
614A THR* 2.7 25.4 + - - -
615A LYS* 3.1 36.2 + - + +
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Residues in contact with GLU 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 4.3 7.1 + - - -
394A TYR* 4.2 21.6 - - + -
446A HIS* 3.7 15.7 - - + +
449A GLN* 3.5 40.3 + - - +
450A GLU* 5.4 3.1 - - - +
597A PRO* 5.5 0.7 - - - +
610A ASP* 3.3 10.0 + - - +
611A HIS* 1.3 89.9 - - + +
613A PHE* 1.3 62.3 + - - +
615A LYS* 3.3 52.8 + - - +
616A LEU* 3.5 7.1 + - - +
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Residues in contact with PHE 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLN* 5.3 0.4 + - - -
496A MET* 3.6 49.1 - - + -
499A CYS* 3.9 16.2 - - + -
500A THR* 4.5 6.1 - - - +
540A LEU* 3.2 36.1 - - + -
543A LEU* 3.6 14.6 - - + -
584A ILE* 4.4 7.2 - - + -
609A PHE* 4.3 15.0 - + - -
610A ASP* 2.9 17.8 + - + +
612A GLU* 1.3 75.8 - - - +
614A THR* 1.3 61.6 + - - +
615A LYS 3.0 0.2 - - - -
616A LEU* 2.9 47.2 + - + +
617A VAL* 3.0 26.0 + - + +
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Residues in contact with THR 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A TYR* 2.6 56.0 + - + +
593A ALA* 3.7 26.9 - - + -
594A SER* 3.4 22.9 + - - +
609A PHE* 4.4 8.3 - - + -
610A ASP 3.2 13.8 + - - +
611A HIS* 2.7 17.0 + - - +
613A PHE* 1.3 76.3 - - - +
615A LYS* 1.3 59.8 + - - +
617A VAL* 3.5 1.0 + - - -
618A LYS* 3.1 15.5 + - - +
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Residues in contact with LYS 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 5.4 2.4 - - - +
394A TYR* 4.8 8.3 + - - -
594A SER 6.0 0.4 - - - +
611A HIS* 3.1 41.3 + - + +
612A GLU* 3.4 37.5 + - - +
613A PHE 3.0 0.4 - - - -
614A THR* 1.3 79.4 - - - +
616A LEU* 1.3 59.9 + - - +
618A LYS* 3.9 9.2 - - + +
619A GLU* 3.0 29.3 + - - +
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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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499A CYS* 4.2 13.7 - - + -
500A THR* 4.0 21.3 - - + +
503A SER* 3.7 31.2 - - - +
543A LEU* 4.5 7.6 - - + -
547A ILE* 4.7 0.7 - - + -
612A GLU 3.5 7.6 + - - +
613A PHE* 2.9 38.6 + - + +
615A LYS* 1.3 76.0 - - - +
617A VAL* 1.3 66.7 + - - +
619A GLU* 3.2 13.4 + - - +
620A LEU* 2.9 43.9 + - + +
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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
----------------------------------------------------------
543A LEU* 3.9 17.5 - - + -
581A LEU* 5.8 0.4 - - + +
584A ILE* 4.1 24.2 - - + -
585A SER 4.8 1.6 - - - +
590A TYR* 3.5 25.8 - - + +
613A PHE* 3.0 45.4 + - + +
614A THR 3.5 0.7 - - - +
616A LEU* 1.3 76.1 - - - +
618A LYS* 1.3 60.4 + - - +
620A LEU 3.0 1.2 + - - -
621A GLU* 2.8 58.2 + - + +
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Residues in contact with LYS 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A TYR* 3.5 7.8 + - + +
614A THR 3.1 14.2 + - - +
615A LYS* 3.9 9.0 - - - +
617A VAL* 1.3 79.4 - - - +
619A GLU* 1.3 62.6 + - - +
621A GLU* 4.4 6.8 + - - +
622A GLY 5.0 3.8 + - - -
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Residues in contact with GLU 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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450A GLU* 5.6 1.9 - - - +
503A SER* 5.0 1.6 + - - -
504A ASN* 4.0 16.3 + - - -
615A LYS* 3.0 21.5 + - - +
616A LEU* 3.5 13.0 - - - +
617A VAL 3.1 0.4 - - - -
618A LYS* 1.3 78.9 - - - +
620A LEU* 1.3 80.4 + - + +
622A GLY* 5.0 0.7 + - - -
623A VAL* 4.2 13.9 + - - +
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A SER* 4.2 7.6 - - - +
504A ASN* 5.2 0.2 - - - +
543A LEU* 4.6 4.5 - - + -
547A ILE* 4.0 29.2 - - + -
550A TYR* 4.8 2.2 - - + -
551A PHE* 3.8 31.0 - - + -
616A LEU* 2.9 35.9 + - + +
617A VAL 4.3 0.2 - - - +
619A GLU* 1.3 99.2 - - + +
621A GLU* 1.3 67.5 + - - +
622A GLY 3.3 2.9 - - - -
623A VAL* 3.2 16.7 + - + +
624A ILE* 2.9 37.2 + - + +
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Residues in contact with GLU 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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543A LEU* 5.1 3.5 - - + +
578A ILE 5.6 0.2 - - - +
581A LEU* 4.3 28.8 - - + +
582A GLY* 3.7 15.9 + - - -
585A SER* 3.6 25.7 + - - -
586A LYS* 5.8 0.3 + - - -
617A VAL* 2.8 36.5 + - + +
618A LYS* 4.4 5.6 + - - +
619A GLU 3.8 0.2 - - - -
620A LEU* 1.3 76.9 - - - +
622A GLY* 1.3 61.9 + - - +
624A ILE* 3.9 6.4 - - - +
625A THR* 3.0 31.2 + - - +
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Residues in contact with GLY 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 LYS 5.0 4.2 + - - -
619A GLU 5.0 1.2 + - - -
620A LEU 3.3 0.6 - - - -
621A GLU* 1.3 80.0 - - - +
623A VAL* 1.3 61.0 + - - +
625A THR* 3.3 8.3 + - - -
626A LYS* 3.1 23.0 + - - +
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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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550A TYR* 3.6 43.1 - - + +
619A GLU 4.2 10.7 + - - +
620A LEU* 3.2 26.6 + - + +
622A GLY* 1.3 75.6 - - - +
624A ILE* 1.3 56.6 + - + +
626A LYS* 3.2 8.7 + - - +
627A ALA* 2.8 35.3 + - - +
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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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543A LEU* 3.8 28.9 - - + +
546A GLY* 3.9 41.3 - - - +
547A ILE* 4.0 9.9 - - + +
550A TYR* 4.2 14.4 - - + -
577A PHE* 4.6 2.2 - - + -
581A LEU* 3.8 22.0 - - + -
620A LEU* 2.9 30.2 + - + +
621A GLU* 3.9 2.9 - - - +
623A VAL* 1.3 78.1 - - + +
625A THR* 1.3 58.9 + - - +
627A ALA* 3.5 6.9 + - - +
628A ILE* 2.9 38.9 + - + +
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Residues in contact with THR 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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578A ILE* 3.8 45.1 - - + +
581A LEU* 4.0 7.4 - - - +
621A GLU* 3.0 18.6 + - - +
622A GLY* 3.5 10.7 - - - -
624A ILE* 1.3 72.1 - - - +
626A LYS* 1.3 66.7 + - - +
628A ILE* 3.2 9.9 + - - +
629A TYR* 3.2 20.4 - - + -
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Residues in contact with LYS 626 (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 GLY 3.1 13.1 + - - +
623A VAL* 3.2 12.5 + - - +
625A THR* 1.3 78.4 - - - +
627A ALA* 1.3 61.7 + - - +
628A ILE 3.3 1.0 + - - -
629A TYR* 3.4 22.9 + - - +
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Residues in contact with ALA 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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549A ILE* 5.1 4.8 - - + +
550A TYR* 3.8 29.2 - - + -
561A LYS* 6.3 2.5 - - - -
565A LYS* 3.1 26.7 - - - -
623A VAL 2.8 16.9 + - - +
624A ILE* 3.8 5.4 - - - +
625A THR 3.2 0.2 - - - -
626A LYS* 1.3 73.0 - - - +
628A ILE* 1.3 59.7 + - + +
629A TYR* 3.1 9.4 + - - -
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Residues in contact with ILE 628 (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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546A GLY* 5.3 1.1 - - - -
549A ILE* 3.8 35.9 - - + -
565A LYS* 3.8 10.8 - - + +
568A ILE* 4.2 11.0 - - + -
574A LYS* 3.3 50.6 + - + +
577A PHE* 4.0 23.6 - - + -
578A ILE* 4.1 15.5 - - + -
624A ILE* 2.9 25.8 - - + +
625A THR 3.2 11.9 + - - +
627A ALA* 1.3 80.6 - - + +
629A TYR* 1.3 61.2 + - + +
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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