Contacts of the helix formed by residues 611 - 631 (chain A) in PDB entry 1K4S
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 ASN 611 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A ASP 3.7 1.1 + - - -
610A GLU* 1.3 73.8 - - - +
612A ILE* 1.3 56.2 + - - +
613A PRO* 3.4 11.7 - - + -
614A ALA* 3.0 14.7 + - + +
615A LYS* 2.5 36.2 + - - +
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Residues in contact with ILE 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A GLU 4.8 4.5 - - - +
611A ASN* 1.3 71.8 - - - +
613A PRO* 1.3 67.1 - - + +
615A LYS* 2.8 14.4 + - + +
616A ILE* 2.5 55.7 + - + +
736A TRP 5.1 6.7 - - - +
737A GLY 4.5 18.4 - - - +
738A VAL* 4.8 14.1 - - + -
739A PRO* 4.7 16.8 - - + -
742A LYS* 5.9 1.1 - - + -
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Residues in contact with PRO 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ASN* 3.5 11.2 - - + -
612A ILE* 1.3 96.7 - - + +
614A ALA* 1.3 63.2 + - - +
616A ILE* 3.2 19.8 - - + +
617A LEU* 3.1 18.0 + - - +
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Residues in contact with ALA 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A GLU* 4.7 6.1 - - + -
611A ASN* 3.0 22.6 + - + +
613A PRO* 1.3 76.0 - - - +
615A LYS* 1.3 57.3 + - - +
617A LEU* 2.8 12.6 + - - +
618A SER* 2.7 37.9 + - - +
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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
----------------------------------------------------------
606A THR* 4.3 17.9 - - + -
607A ALA 3.1 24.9 - - - +
608A PRO 4.1 5.8 + - - -
610A GLU* 3.4 28.8 + - + +
611A ASN 2.5 25.8 + - - +
612A ILE* 3.0 20.8 - - + +
614A ALA* 1.3 70.1 - - - +
616A ILE* 1.3 50.9 + - + +
618A SER* 2.9 11.2 - - - +
619A TYR* 2.7 34.8 + - - +
732A TRP* 4.3 14.5 - - + -
736A TRP* 3.3 46.5 + - - +
738A VAL* 4.9 8.4 - - + +
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Residues in contact with ILE 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ILE* 2.5 40.2 + - + +
613A PRO* 3.2 27.8 - - + +
615A LYS* 1.3 71.8 - - + +
617A LEU* 1.3 57.1 + - - +
619A TYR* 2.7 30.0 + - - +
620A ASN* 2.8 24.5 - - - +
732A TRP* 5.1 2.2 - - - -
738A VAL* 5.2 4.7 - - + -
742A LYS* 5.0 11.0 - - + +
743A ILE* 4.5 24.5 - - + -
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Residues in contact with LEU 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A PRO 3.1 7.3 + - - +
614A ALA* 2.8 14.7 + - - +
616A ILE* 1.3 76.4 - - - +
618A SER* 1.3 63.6 + - - +
619A TYR 2.9 1.7 + - - -
620A ASN* 2.9 22.3 + - + +
621A ARG* 2.9 61.2 + - + +
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Residues in contact with SER 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A LEU* 4.8 2.7 - - - +
605A LEU* 3.6 17.0 + - - +
606A THR* 4.9 8.0 + - - -
607A ALA* 5.2 2.8 + - - +
610A GLU* 5.1 5.2 - - - +
614A ALA* 2.7 23.4 + - - +
615A LYS* 2.9 19.6 - - - -
617A LEU* 1.3 72.5 - - - +
619A TYR* 1.3 61.0 + - - +
621A ARG* 3.2 42.6 + - - +
622A ALA* 3.5 14.0 + - - +
732A TRP* 6.1 0.2 - - - -
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Residues in contact with TYR 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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598A LEU* 5.3 3.3 - - + +
602A LEU* 3.4 37.9 - - + +
615A LYS 2.7 14.2 + - - +
616A ILE* 2.7 17.0 + - - +
618A SER* 1.3 68.6 - - - +
620A ASN* 1.3 64.9 + - - -
622A ALA* 2.7 22.3 + - - +
623A ASN* 2.6 49.1 + - - +
720A LYS* 5.9 1.7 - - - +
729A THR* 3.0 41.7 + - + +
732A TRP* 3.4 33.0 - + + -
743A ILE* 3.8 26.7 - - + +
744A TYR* 4.3 3.6 + - - -
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Residues in contact with ASN 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ILE* 2.8 36.6 - - - +
617A LEU* 2.9 18.3 + - + +
619A TYR* 1.3 83.2 - - - +
621A ARG* 1.3 63.1 + - - +
623A ASN* 3.0 23.9 + - - +
624A ARG* 3.3 9.5 + - - +
743A ILE* 5.7 1.1 - - - +
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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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605A LEU* 2.8 51.7 + - + +
617A LEU* 2.9 47.0 + - + +
618A SER* 3.2 28.4 + - - +
620A ASN* 1.3 76.6 - - - +
622A ALA* 1.3 62.7 + - - +
624A ARG* 3.4 25.8 - - - +
625A ALA* 3.8 4.2 + - - +
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Residues in contact with ALA 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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598A LEU* 5.7 2.7 - - + -
601A GLN* 3.4 31.6 - - + +
602A LEU* 4.1 21.3 - - + +
605A LEU* 4.1 7.8 - - + +
618A SER 3.5 4.9 + - - +
619A TYR 2.7 18.1 + - - +
621A ARG* 1.3 78.3 - - - +
623A ASN* 1.3 62.1 + - - +
625A ALA* 3.2 16.3 + - - +
626A VAL* 3.2 16.0 - - - +
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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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598A LEU* 4.1 15.9 - - - +
602A LEU* 5.8 0.2 - - - +
619A TYR* 2.6 63.4 + - - +
620A ASN* 3.0 9.2 + - - +
622A ALA* 1.3 74.2 - - - +
624A ARG* 1.3 65.5 + - - +
626A VAL* 3.1 26.2 + - + +
627A ALA* 3.3 8.1 + - - +
719A SER* 5.8 4.9 + - - +
720A LYS* 5.8 6.9 - - - +
724A LEU* 6.0 2.6 - - - +
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Residues in contact with ARG 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 ASN 3.3 7.2 + - - +
621A ARG* 3.4 20.0 - - - +
622A ALA 3.2 0.4 - - - -
623A ASN* 1.3 77.3 - - - +
625A ALA* 1.3 64.5 + - - +
626A VAL 3.1 1.0 + - - -
627A ALA* 3.3 5.2 + - - +
628A ILE* 3.3 31.9 + - + +
710A GLU* 2.8 28.9 + - - -
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Residues in contact with ALA 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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597A THR* 5.9 1.2 - - - -
601A GLN* 3.6 25.1 - - + +
605A LEU* 5.5 2.7 - - + -
621A ARG 3.8 4.2 + - - +
622A ALA 3.2 13.6 + - - +
624A ARG* 1.3 80.9 - - - +
626A VAL* 1.3 57.4 + - - +
628A ILE* 2.8 38.2 - - + +
629A LEU* 4.0 2.8 - - - +
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Residues in contact with VAL 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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594A ALA* 3.7 10.3 - - + +
597A THR* 3.7 21.1 - - - +
598A LEU* 4.0 26.0 - - + -
601A GLN* 4.7 2.2 - - + -
622A ALA 3.2 19.3 - - - +
623A ASN* 3.2 17.5 - - + +
624A ARG 3.0 0.2 - - - -
625A ALA* 1.3 72.6 - - - +
627A ALA* 1.3 55.2 + - - +
628A ILE 2.8 14.4 + - - -
629A LEU* 2.9 26.8 - - + +
630A CYS* 4.4 5.3 + - - -
719A SER* 5.7 6.3 - - - +
724A LEU* 3.6 26.9 - - + -
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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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623A ASN 3.3 5.9 + - - +
624A ARG* 3.3 8.4 + - - +
626A VAL* 1.3 74.2 - - - +
628A ILE* 1.3 55.6 + - - +
629A LEU 3.0 12.0 + - - -
630A CYS* 3.4 20.3 + - + +
631A ASN* 3.6 10.4 + - - -
632A HIS* 4.3 21.0 + - + -
714A ILE* 6.1 8.3 - - + -
719A SER* 5.7 9.6 - - - -
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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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624A ARG* 3.3 31.2 + - + +
625A ALA* 2.8 26.5 - - - +
626A VAL 2.8 0.8 + - - -
627A ALA* 1.3 77.7 - - - +
629A LEU* 1.3 68.5 + - + +
631A ASN* 4.7 3.3 + - - -
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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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484A LYS 4.4 13.0 - - - +
485A LEU* 3.9 15.8 - - - +
486A ALA* 4.2 20.2 - - + -
537A TYR* 4.7 5.4 + - - -
593A ASN* 4.8 19.7 - - + -
594A ALA* 5.6 3.8 - - - +
597A THR* 4.8 16.8 - - + +
625A ALA 4.0 3.4 - - - +
626A VAL* 2.9 27.4 - - + +
628A ILE* 1.3 92.8 - - + +
630A CYS* 1.3 69.3 - - - +
631A ASN* 3.0 11.8 + - - +
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Residues in contact with CYS 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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485A LEU 5.1 0.7 - - - -
486A ALA* 5.0 10.5 - - - -
537A TYR* 4.7 4.9 - - - -
590A ARG* 3.9 23.5 + - - +
594A ALA* 5.8 8.3 - - - -
626A VAL* 4.7 3.6 - - - -
627A ALA* 3.4 15.1 + - - +
629A LEU* 1.3 87.6 - - - +
631A ASN* 1.3 63.7 - - - +
632A HIS* 2.8 44.2 + - + +
719A SER* 6.1 4.9 - - - -
723A PTR 6.4 4.0 - - - -
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Residues in contact with ASN 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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536A ARG 4.5 6.6 - - - +
537A TYR* 3.7 35.4 + - + -
538A TYR 3.8 25.2 + - - +
539A ASN* 4.7 6.7 + - - +
627A ALA 3.6 7.3 + - - -
628A ILE 5.4 2.4 + - - -
629A LEU* 3.0 7.5 + - - +
630A CYS* 1.3 78.4 - - - +
632A HIS* 1.3 67.4 + - - +
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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
------------------------------------------------------------
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