Contacts of the helix formed by residues 617 - 633 (chain A) in PDB entry 2KIS
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 SER 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A GLY 3.7 21.9 + - - +
616A GLY* 1.3 80.7 - - - +
618A LEU* 1.3 66.2 + - - +
619A GLU* 4.5 0.6 - - - +
620A ALA* 4.2 1.4 - - - +
621A ARG* 4.2 16.9 + - - +
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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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617A SER* 1.3 78.2 - - - +
619A GLU* 1.3 67.8 + - - +
620A ALA 3.1 2.0 - - - -
621A ARG* 2.9 28.3 + - - +
622A MET* 2.9 24.7 + - + +
656A LEU* 3.7 25.4 - - + -
657A ASN* 6.1 2.2 - - - +
660A GLU* 3.5 27.8 - - + +
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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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613A GLY 5.9 0.2 + - - -
614A ALA* 4.9 2.4 + - - -
615A MET* 3.6 52.5 + - + +
616A GLY 4.6 0.7 - - - +
617A SER 3.6 0.4 - - - +
618A LEU* 1.3 78.9 - - - +
620A ALA* 1.3 55.9 + - - +
622A MET* 3.3 11.0 + - - +
623A LYS* 2.8 32.4 + - - +
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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
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615A MET* 4.9 2.2 - - - +
616A GLY* 4.0 32.6 - - - +
617A SER 4.2 2.9 + - - +
618A LEU 3.1 0.6 - - - -
619A GLU* 1.3 80.0 - - - +
621A ARG* 1.3 56.4 + - - +
623A LYS* 3.0 8.8 + - - +
624A GLN* 2.8 42.3 + - - +
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Residues in contact with ARG 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 SER 4.2 12.1 + - - +
618A LEU* 2.9 28.6 + - + +
620A ALA* 1.3 74.1 - - - +
622A MET* 1.3 60.1 + - - +
623A LYS 2.9 9.7 + - - -
624A GLN* 3.1 22.1 + - - +
625A PHE* 3.1 9.4 + - - +
655A LEU* 3.6 59.4 + - + +
656A LEU* 3.6 15.5 - - + +
657A ASN* 5.8 3.1 - - - +
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Residues in contact with MET 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* 2.9 19.3 + - + +
619A GLU* 3.5 11.9 - - - +
621A ARG* 1.3 75.0 - - - +
623A LYS* 1.3 56.0 + - - +
625A PHE* 3.8 2.7 - - - +
626A LYS* 3.3 22.7 + - - +
656A LEU* 3.5 22.2 - - + +
660A GLU* 4.7 6.1 - - - +
663A GLN* 3.1 34.3 - - + +
664A VAL* 3.5 31.9 - - + +
667A GLN* 6.1 3.6 - - + -
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Residues in contact with LYS 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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615A MET* 6.5 1.6 - - - -
619A GLU 2.8 17.5 + - - +
620A ALA* 3.1 12.3 - - - +
621A ARG 2.9 0.2 - - - -
622A MET* 1.3 78.2 - - - +
624A GLN* 1.3 56.5 + - + +
625A PHE 2.9 5.2 - - - -
626A LYS* 3.5 31.3 - - + +
627A ASP* 2.9 34.0 + - + +
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Residues in contact with GLN 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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620A ALA* 2.8 43.3 + - - +
621A ARG* 3.4 13.0 - - - +
623A LYS* 1.3 76.5 - - + +
625A PHE* 1.3 57.2 + - - +
627A ASP* 4.0 6.4 - - - +
628A MET* 3.2 24.4 + - - +
652A ARG* 4.0 15.8 + - - +
655A LEU* 3.9 20.1 - - + +
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Residues in contact with PHE 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 ARG 3.1 4.3 + - - +
622A MET 3.8 4.3 - - - +
623A LYS 2.9 0.4 - - - -
624A GLN* 1.3 76.4 - - - +
626A LYS* 1.3 67.0 + - - +
627A ASP 3.1 1.1 - - - -
628A MET* 3.0 16.7 + - + +
629A LEU* 3.0 49.0 + - + +
640A TRP* 4.5 8.5 - + - -
647A ILE* 5.0 1.1 - - + -
652A ARG 3.4 20.9 - - - -
653A TYR* 3.1 30.3 - + - -
655A LEU* 3.9 7.2 - - + +
656A LEU* 3.6 34.8 - - + -
661A ARG* 3.4 37.0 - - + -
664A VAL* 3.7 19.1 - - + -
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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 MET 3.3 16.0 + - - +
623A LYS* 3.3 34.2 + - + +
625A PHE* 1.3 78.3 - - - +
627A ASP* 1.3 66.6 + - - +
629A LEU* 3.1 17.9 - - + +
630A LEU* 3.2 17.2 + - + +
664A VAL* 4.1 17.2 - - + +
668A TYR* 4.1 25.8 - - + -
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Residues in contact with ASP 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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623A LYS* 2.9 22.9 + - + +
624A GLN* 4.0 7.0 - - - +
626A LYS* 1.3 78.7 - - - +
628A MET* 1.3 57.8 + - - +
630A LEU* 2.7 28.8 + - - +
631A GLU* 2.8 39.2 + - - +
652A ARG* 4.1 9.5 + - - -
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Residues in contact with MET 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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624A GLN 3.2 8.2 + - - +
625A PHE* 3.0 54.6 + - + +
627A ASP* 1.3 79.1 + - - +
629A LEU* 1.3 62.1 + - + +
631A GLU* 2.9 19.6 + - - +
632A ARG* 3.2 15.0 + - - +
647A ILE* 3.5 37.9 - - + +
650A ASP* 4.5 0.7 - - - -
652A ARG* 3.2 55.6 - - - +
653A TYR* 3.8 12.1 - - - -
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Residues in contact with LEU 629 (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 PHE* 3.0 45.4 + - + +
626A LYS* 3.1 10.5 - - - +
628A MET* 1.3 84.1 - - + +
630A LEU* 1.3 56.7 + - - +
633A GLY* 3.0 10.2 + - - -
634A VAL* 3.0 56.3 + - + -
640A TRP* 5.9 1.8 - - + -
647A ILE* 4.6 2.5 - - + -
664A VAL* 3.5 40.4 - - + +
665A PHE* 4.6 5.4 - - + -
668A TYR* 3.3 31.1 + - + -
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Residues in contact with LEU 630 (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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626A LYS* 3.2 16.7 + - + +
627A ASP* 2.7 17.9 + - - +
629A LEU* 1.3 75.0 - - - +
631A GLU* 1.3 67.6 + - - +
633A GLY* 4.1 4.2 + - - -
668A TYR* 3.8 19.7 + - + +
672A ARG* 4.3 26.2 - - - +
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Residues in contact with GLU 631 (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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627A ASP* 2.8 40.5 + - - +
628A MET 2.9 9.6 + - - +
630A LEU* 1.3 86.8 - - - +
632A ARG* 1.3 66.1 + - - +
652A ARG* 3.4 24.1 + - - +
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Residues in contact with ARG 632 (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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628A MET* 3.2 15.3 + - - +
631A GLU* 1.3 80.6 - - - +
633A GLY* 1.3 66.7 + - - +
646A LYS* 3.2 57.5 + - + +
647A ILE* 3.5 31.7 + - + -
649A PHE* 4.7 5.1 - - - +
650A ASP* 2.9 35.1 + - - +
652A ARG* 3.2 31.9 - - - +
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Residues in contact with GLY 633 (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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629A LEU 3.0 12.8 + - - -
630A LEU* 4.1 4.9 - - - -
631A GLU 3.4 2.6 - - - +
632A ARG* 1.3 83.5 - - - +
634A VAL* 1.3 53.9 + - - +
635A SER* 2.7 19.2 + - - -
643A GLU* 3.4 5.0 - - - +
646A LYS* 4.3 8.3 - - - +
668A TYR* 4.4 5.4 - - - -
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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