Contacts of the helix formed by residues 589 - 599 (chain J) in PDB entry 6H25
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 589 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478J VAL* 3.6 5.2 - - - +
479J ASP 3.8 7.2 - - - +
481J PRO* 4.0 29.2 - - + -
588J LEU* 1.3 78.1 - - - +
590J TYR* 1.3 61.1 + - - +
591J ALA* 4.4 3.1 + - - +
592J GLU* 3.2 39.8 + - - +
593J ALA* 3.1 29.8 + - - +
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Residues in contact with TYR 590 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478J VAL* 3.6 31.6 + - + +
479J ASP 3.4 33.7 - - - -
480J PRO* 3.5 13.7 - - + -
481J PRO* 4.9 4.9 - - + +
589J THR* 1.3 74.2 - - - +
591J ALA* 1.3 61.9 + - - +
593J ALA* 4.2 1.0 - - - +
594J GLN* 2.9 31.8 + - - +
657J ARG* 4.9 12.9 - - + +
659J THR* 3.2 32.0 + - - +
660J ASN* 3.3 38.4 + - - +
663J VAL* 4.2 15.0 - - + +
43R U 3.9 14.8 + - - -
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Residues in contact with ALA 591 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589J THR* 3.6 3.0 + - - +
590J TYR* 1.3 77.5 - - - +
592J GLU* 1.3 60.1 + - + +
594J GLN* 3.3 4.9 + - - +
595J LEU* 3.0 41.0 + - + +
657J ARG* 5.6 11.9 - - - +
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Residues in contact with GLU 592 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587J SER 5.7 0.5 - - - +
588J LEU* 5.2 7.4 - - + +
589J THR* 3.2 31.7 + - - +
590J TYR 3.3 0.2 - - - -
591J ALA* 1.3 79.2 - - + +
593J ALA* 1.3 57.4 + - - +
595J LEU* 3.3 7.8 + - - +
596J ARG* 2.9 36.7 + - + +
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Residues in contact with ALA 593 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478J VAL* 4.4 10.8 - - + -
588J LEU* 3.9 25.5 - - + +
589J THR 3.1 19.9 + - - +
590J TYR* 4.2 2.2 - - - +
592J GLU* 1.3 74.9 - - - +
594J GLN* 1.3 61.8 + - - +
596J ARG* 3.4 12.1 - - - +
597J ILE* 2.9 38.8 + - + +
610J LEU* 4.7 6.5 - - + -
659J THR* 5.5 5.8 - - + +
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Residues in contact with GLN 594 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590J TYR 2.9 19.7 + - - +
591J ALA* 3.6 7.2 - - - +
592J GLU 3.2 0.2 - - - -
593J ALA* 1.3 77.0 - - - +
595J LEU* 1.3 63.1 + - + +
597J ILE* 4.9 5.0 - - - +
598J ASP* 2.9 49.7 + - + +
614J ASN* 5.6 5.1 - - - +
657J ARG* 3.8 29.7 - - + +
658J GLU* 4.2 10.8 + - - +
659J THR* 3.4 27.4 + - - +
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Residues in contact with LEU 595 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591J ALA* 3.0 30.8 + - + +
592J GLU* 3.8 6.1 - - - +
594J GLN* 1.3 79.8 - - + +
596J ARG* 1.3 64.2 + - - +
598J ASP* 4.2 3.1 - - - -
599J SER* 3.3 25.8 + - - +
602J MET* 4.9 4.1 - - - +
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Residues in contact with ARG 596 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588J LEU* 4.3 22.7 - - - +
592J GLU* 2.9 23.0 + - + +
593J ALA* 3.4 17.3 - - - +
594J GLN 3.2 0.2 - - - -
595J LEU* 1.3 78.0 - - - +
597J ILE* 1.3 60.3 + - + +
599J SER 2.9 21.7 - - - +
602J MET* 4.5 24.3 - - + +
604J ASP* 4.9 9.7 + - - +
606J ILE* 3.8 17.8 - - - +
607J THR* 2.7 49.3 + - + +
610J LEU* 4.5 8.4 - - + +
611J ARG* 3.1 10.9 + - - -
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Residues in contact with ILE 597 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593J ALA* 2.9 21.4 + - + +
594J GLN* 4.2 6.1 - - - +
596J ARG* 1.3 76.4 - - + +
598J ASP* 1.3 63.4 + - - +
599J SER 3.2 2.4 + - - +
607J THR* 4.5 0.9 - - - +
610J LEU* 3.7 48.0 - - + +
611J ARG* 3.4 36.3 + - + +
614J ASN* 3.4 34.3 - - + +
659J THR* 4.1 23.8 - - + -
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Residues in contact with ASP 598 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594J GLN* 2.9 34.4 + - + +
595J LEU* 4.8 2.2 - - - -
597J ILE* 1.3 78.2 - - - +
599J SER* 1.3 57.5 + - - +
600J ALA 4.1 0.7 + - - -
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Residues in contact with SER 599 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595J LEU* 3.3 19.0 + - - -
596J ARG 2.9 7.3 - - - +
597J ILE 3.2 2.7 - - - +
598J ASP* 1.3 80.1 - - - +
600J ALA* 1.3 50.4 + - - +
601J ASN* 1.1 56.7 + - - +
602J MET* 4.4 6.2 + - - +
611J ARG* 2.5 29.3 + - - -
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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