Contacts of the helix formed by residues 675 - 687 (chain I) in PDB entry 6PST
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 675 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674I ASP* 1.3 74.0 - - - +
676I ALA* 1.3 71.2 + - - +
677I ASN* 3.5 25.5 + - - +
678I ARG* 2.9 26.9 + - + +
679I ALA 3.1 8.1 + - - -
1107I MET* 2.7 45.7 + - + +
744J ARG* 4.0 19.9 + - - +
763J PHE* 4.0 8.7 - - + -
772J TYR* 3.7 0.2 + - - -
779J ALA* 5.2 4.2 - - - +
5N ALA* 5.7 1.6 - - - +
9N TYR* 5.7 4.6 - - - +
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Residues in contact with ALA 676 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561I ILE* 4.4 7.7 - - + +
674I ASP 3.5 1.8 + - - -
675I ASP* 1.3 78.7 + - - +
677I ASN* 1.3 59.3 + - - +
679I ALA* 3.1 5.5 + - - +
680I LEU* 3.0 24.1 + - - +
744J ARG* 5.5 2.0 - - - +
772J TYR* 3.3 24.3 - - + +
775J SER* 4.8 6.3 - - - +
776J THR* 4.1 24.9 - - + +
779J ALA* 3.8 20.6 - - + -
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Residues in contact with ASN 677 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675I ASP* 3.2 14.3 + - - +
676I ALA* 1.3 74.5 - - - +
678I ARG* 1.3 61.9 + - - +
680I LEU* 3.1 12.0 + - - +
681I MET* 2.9 33.8 + - - +
779J ALA* 3.3 41.7 + - - +
780J ARG* 4.4 0.5 + - - -
783J LEU* 3.4 26.9 - - + +
5N ALA* 4.2 18.6 + - + -
8N ALA* 3.9 21.6 - - - +
9N TYR* 5.2 1.0 - - - +
12N THR* 5.4 0.4 + - - -
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Residues in contact with ARG 678 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674I ASP* 4.4 2.5 - - + -
675I ASP* 2.9 27.2 + - + +
677I ASN* 1.3 75.8 - - - +
679I ALA* 1.3 58.2 + - - +
681I MET* 3.3 18.6 + - - +
682I GLY* 2.8 25.5 + - - -
1070I HIS 3.9 14.0 - - - +
1071I GLY* 3.6 19.4 + - - -
1106I ARG* 3.2 27.9 - - + +
1107I MET 4.7 0.4 - - - -
1108I ASN* 3.6 36.8 - - + +
3N ASP* 2.3 27.9 + - - -
5N ALA* 3.1 24.2 + - - +
6N ASP* 2.6 30.7 + - - -
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Residues in contact with ALA 679 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561I ILE* 3.5 21.5 - - + +
668I ILE* 3.8 11.0 - - + +
671I LEU* 3.3 34.1 - - + -
674I ASP* 4.6 4.6 - - + +
675I ASP 3.1 5.5 + - - -
676I ALA 3.1 6.0 + - - +
678I ARG* 1.3 77.7 - - - +
680I LEU* 1.3 61.4 + - - +
683I ALA* 2.9 21.1 + - - +
1070I HIS* 5.7 0.7 - - - +
772J TYR* 3.3 15.0 - - - +
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Residues in contact with LEU 680 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560I PRO 5.1 2.5 - - - +
561I ILE* 3.3 32.6 - - - +
563I THR* 3.4 35.7 - - + +
565I GLU* 3.8 29.2 - - + +
569I ILE* 4.9 4.0 - - + -
676I ALA 3.0 12.2 + - - +
677I ASN* 3.1 15.2 + - - +
679I ALA* 1.3 76.0 - - - +
681I MET* 1.3 65.2 + - + +
683I ALA* 3.8 0.7 - - - +
684I ASN* 2.4 37.9 + - - +
780J ARG* 5.2 6.1 - - + +
783J LEU* 3.8 21.3 - - + -
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Residues in contact with MET 681 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565I GLU* 5.2 15.3 - - + +
677I ASN* 2.9 16.3 + - + +
678I ARG* 3.7 29.2 - - - +
680I LEU* 1.3 84.8 - - + +
682I GLY* 1.3 59.6 + - - +
684I ASN* 3.3 5.3 + - - +
685I MET* 2.9 44.1 + - + +
1071I GLY* 4.2 6.1 - - - +
1073I LYS* 3.4 34.1 - - + -
783J LEU* 5.7 2.0 - - + -
3N ASP 3.7 18.4 - - - +
4N GLU* 5.3 4.3 - - + -
5N ALA* 4.0 12.3 - - + -
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Residues in contact with GLY 682 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668I ILE* 4.5 1.1 - - - -
678I ARG 2.8 13.8 + - - -
679I ALA 3.8 1.1 - - - -
680I LEU 3.3 0.2 - - - -
681I MET* 1.3 77.7 - - - +
683I ALA* 1.3 56.6 + - - +
685I MET* 3.3 3.4 + - - +
686I GLN* 2.9 33.4 + - - +
1068I GLY 4.6 1.9 - - - +
1069I ARG* 3.7 16.5 - - - +
1071I GLY* 3.4 24.1 - - - -
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Residues in contact with ALA 683 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521I LEU* 5.2 1.4 - - - +
561I ILE* 4.5 4.7 - - + -
562I GLU* 4.1 23.3 - - + +
664I GLY* 4.4 2.3 - - - -
665I ALA* 4.2 22.9 - - + +
668I ILE* 4.1 2.5 - - + +
679I ALA 2.9 16.5 + - - +
680I LEU 3.8 3.1 - - - +
682I GLY* 1.3 77.2 - - - +
684I ASN* 1.3 64.6 + - - +
685I MET 3.1 0.2 + - - -
686I GLN* 3.1 14.2 + - - +
687I ARG* 3.1 25.7 + - - +
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Residues in contact with ASN 684 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563I THR 3.0 34.4 + - - +
564I PRO* 3.6 6.9 - - - +
565I GLU* 4.1 14.8 - - - +
680I LEU* 2.4 45.3 + - - +
681I MET* 3.9 4.5 - - - +
683I ALA* 1.3 77.4 - - - +
685I MET* 1.3 60.8 + - + +
687I ARG* 2.4 51.3 + - - +
688I GLN* 3.5 21.8 + - - +
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Residues in contact with MET 685 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681I MET* 2.9 30.0 + - + +
682I GLY* 3.9 3.6 - - - +
684I ASN* 1.3 77.7 - - + +
686I GLN* 1.3 59.7 + - - +
687I ARG 3.1 1.3 - - - -
688I GLN* 3.0 26.1 + - - +
689I ALA* 3.5 1.4 + - - +
1065I LYS* 4.6 3.1 - - - +
1067I ALA* 3.9 8.1 - - + -
1068I GLY 4.8 4.5 - - - +
1071I GLY* 3.8 26.2 - - - +
1073I LYS* 3.4 48.0 - - + +
1233I LEU* 4.5 1.3 - - - +
1235I LEU* 3.0 47.2 - - + +
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Residues in contact with GLN 686 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519I ASN* 3.7 14.0 + - - +
521I LEU* 4.2 10.7 - - + +
664I GLY 3.5 21.0 - - - +
667I LEU* 4.0 16.1 + - - +
668I ILE* 3.9 13.7 - - - +
682I GLY 2.9 19.7 + - - +
683I ALA* 3.1 6.5 + - - +
685I MET* 1.3 76.1 - - - +
687I ARG* 1.3 63.0 + - - +
688I GLN 3.2 0.7 + - - -
689I ALA* 3.6 6.9 + - - +
796I LEU* 3.8 26.9 - - + +
1068I GLY 5.6 0.2 - - - +
1069I ARG* 3.2 42.2 - - + +
1233I LEU* 3.8 20.6 - - + -
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Residues in contact with ARG 687 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516I ASP* 5.6 4.7 + - - -
518I ASN* 3.4 13.0 + - - +
519I ASN* 3.9 0.8 + - - -
521I LEU* 4.5 8.1 - - + -
522I SER* 3.4 28.8 - - - +
525I THR* 3.2 36.4 + - + -
529I ARG* 4.0 20.9 - - - +
562I GLU* 2.2 42.0 + - - +
563I THR* 5.1 0.8 - - - +
564I PRO* 4.8 9.5 - - - +
683I ALA 3.1 10.3 + - - +
684I ASN* 2.4 51.1 + - - +
685I MET 3.1 0.4 - - - -
686I GLN* 1.3 79.1 - - - +
688I GLN* 1.3 60.7 + - + +
689I ALA 3.5 0.2 - - - -
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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