Contacts of the helix formed by residues 641 - 653 (chain A) in PDB entry 3KSS
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 THR 641 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A GLN* 5.3 2.2 - - - +
639A GLY 3.1 4.2 + - - -
640A MET* 1.3 73.9 - - - +
642A MET* 1.3 78.4 + - - +
643A ASP* 3.9 9.2 + - + +
644A LYS* 3.0 24.8 + - + +
645A ILE* 2.8 25.3 + - - +
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Residues in contact with MET 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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566A ASN* 3.6 37.5 - - + +
567A GLU 4.8 3.4 - - - +
568A GLY* 5.5 1.1 - - - +
570A LEU* 4.5 9.9 - - + -
630A LEU* 3.8 29.8 - - + -
633A GLN* 5.2 11.6 - - - +
641A THR* 1.3 78.2 + - - +
643A ASP* 1.3 66.1 + - - +
645A ILE* 3.0 12.0 + - + +
646A ILE* 2.9 55.5 + - + +
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Residues in contact with ASP 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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641A THR* 3.5 8.3 + - + +
642A MET* 1.3 83.5 - - - +
644A LYS* 1.3 56.2 + - - +
646A ILE* 3.5 13.5 - - + +
647A GLU* 2.9 29.5 + - - +
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Residues in contact with LYS 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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640A MET* 3.3 32.8 - - + +
641A THR* 3.0 34.4 + - + +
643A ASP* 1.3 75.4 - - - +
645A ILE* 1.3 67.3 + - - +
647A GLU* 3.1 21.7 + - - +
648A GLU* 3.0 22.2 + - - +
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Residues in contact with ILE 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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570A LEU* 5.6 2.2 - - + -
599A VAL* 4.9 4.9 - - + -
601A GLU* 3.0 52.3 - - + +
602A VAL* 5.5 1.1 - - + -
630A LEU* 5.1 16.4 - - + -
633A GLN* 4.8 11.4 - - - +
640A MET* 3.4 13.8 - - + +
641A THR 2.8 23.7 + - - +
642A MET* 3.2 13.2 - - + +
644A LYS* 1.3 73.0 - - - +
646A ILE* 1.3 69.4 + - + +
648A GLU* 2.9 7.1 + - - +
649A LEU* 2.8 45.7 + - + +
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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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570A LEU* 3.3 34.1 - - + -
642A MET* 2.9 48.4 + - + +
643A ASP* 3.5 15.0 - - + +
645A ILE* 1.3 75.9 - - + +
647A GLU* 1.3 56.9 + - - +
649A LEU* 3.0 10.4 + - - +
650A ASP* 2.8 36.1 + - + +
662A TRP* 4.4 28.2 + - + -
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Residues in contact with GLU 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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643A ASP 2.9 17.8 + - - +
644A LYS* 3.4 28.4 + - - +
646A ILE* 1.3 77.1 - - - +
648A GLU* 1.3 65.2 + - - +
650A ASP* 3.2 5.4 + - - +
651A ASN* 2.9 29.1 + - + +
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Residues in contact with GLU 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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599A VAL* 3.2 36.0 - - + +
600A PRO* 4.6 1.7 - - - +
601A GLU* 3.8 9.9 - - - +
637A ARG* 4.0 16.0 + - - -
640A MET* 4.6 10.6 - - + +
644A LYS 3.0 11.0 + - - +
645A ILE* 2.9 14.4 + - - +
647A GLU* 1.3 72.5 - - - +
649A LEU* 1.3 52.8 + - - +
651A ASN* 3.0 8.2 + - + +
652A THR* 2.6 49.6 + - - +
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Residues in contact with LEU 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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570A LEU* 5.4 4.0 - - + -
596A ILE* 3.9 29.8 - - + +
599A VAL* 3.5 32.8 - - + -
602A VAL* 5.0 5.6 - - + -
628A ILE* 5.4 2.0 - - + -
645A ILE* 2.8 56.0 + - + +
646A ILE* 3.4 8.3 - - - +
648A GLU* 1.3 73.9 - - + +
650A ASP* 1.3 58.6 + - - +
652A THR* 2.9 20.5 + - - -
653A VAL* 2.9 19.3 + - + +
662A TRP* 3.4 33.2 - - + -
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Residues in contact with ASP 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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646A ILE* 2.8 22.0 + - + +
647A GLU* 3.7 7.0 - - - +
649A LEU* 1.3 73.8 - - - +
651A ASN* 1.3 59.1 + - - +
653A VAL 3.6 12.0 - - - +
654A ARG* 4.8 5.0 - - - +
660A ASN* 3.6 23.4 + - - +
662A TRP* 3.7 28.6 - - + +
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Residues in contact with ASN 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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647A GLU* 2.9 20.7 + - + +
648A GLU* 3.5 6.2 - - - +
650A ASP* 1.3 78.5 - - - +
652A THR* 1.3 61.2 + - - +
653A VAL 4.8 0.7 - - - -
654A ARG* 4.7 8.4 - - - +
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Residues in contact with THR 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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595A LEU* 4.0 22.1 - - + +
598A SER* 4.1 20.4 - - - +
599A VAL* 4.5 5.0 - - + +
648A GLU* 2.6 42.1 + - - +
649A LEU* 2.9 9.1 + - + -
651A ASN* 1.3 77.7 - - - +
653A VAL* 1.3 64.2 + - + +
654A ARG* 3.6 3.3 + - - +
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Residues in contact with VAL 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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572A TYR* 4.0 27.4 - - + +
592A THR* 4.6 11.9 - - + +
595A LEU* 3.5 33.0 - - + -
596A ILE* 3.6 30.7 - - + +
649A LEU* 2.9 12.4 + - + +
650A ASP 3.6 3.4 - - - +
652A THR* 1.3 77.3 - - + +
654A ARG* 1.3 57.8 + - - +
655A LEU* 4.3 15.5 - - + +
660A ASN* 2.6 34.9 + - - +
662A TRP* 5.2 0.7 - - + -
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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