Contacts of the helix formed by residues 627 - 645 (chain A) in PDB entry 6T2C
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 627 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609A ASN 4.9 3.4 - - - -
610A ARG* 5.1 3.1 - - - -
611A GLU 3.5 35.2 - - - +
612A ASN* 4.0 9.4 - - - +
613A ASP 4.7 0.4 - - - +
614A TRP* 4.2 4.0 - - - -
626A GLY* 1.3 78.3 - - - +
628A ILE* 1.3 66.7 + - - +
629A GLY* 3.3 10.2 + - - -
630A LYS* 3.5 12.7 + - - +
631A VAL* 3.4 21.0 + - - +
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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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440A PHE* 4.2 19.1 - - + -
587A VAL* 5.0 4.7 - - + -
590A MET* 5.4 2.0 - - + -
606A PHE* 3.9 45.3 - - + +
607A PHE* 4.1 22.9 - - + +
609A ASN* 5.1 11.8 + - + +
614A TRP* 3.9 30.1 - - + +
627A THR* 1.3 74.7 - - - +
629A GLY* 1.3 62.4 + - - +
631A VAL* 3.1 14.3 + - + +
632A CYS* 3.0 33.8 + - - -
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Residues in contact with GLY 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PHE* 5.1 2.2 - - - -
444A GLU* 3.6 28.5 - - - +
627A THR* 3.3 6.0 + - - -
628A ILE* 1.3 79.8 - - - +
630A LYS* 1.3 59.1 + - - +
632A CYS* 3.2 7.0 + - - +
633A ARG* 3.0 41.5 + - - +
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Residues in contact with LYS 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASN 5.1 1.2 + - - -
410A SER* 3.8 26.3 + - - +
411A GLU* 4.8 9.7 - - - +
616A ILE* 4.1 31.6 - - + -
626A GLY* 4.6 3.4 - - - -
627A THR* 3.5 24.5 + - - +
628A ILE 3.3 0.4 - - - -
629A GLY* 1.3 75.4 - - - +
631A VAL* 1.3 57.4 + - - +
633A ARG* 3.5 26.1 + - - +
634A VAL* 2.9 51.0 + - + +
1B MET* 4.9 7.1 - - - -
3B VAL* 4.5 13.8 - - - +
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Residues in contact with VAL 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A VAL* 5.1 2.0 - - + -
590A MET* 4.9 9.0 - - + -
614A TRP* 3.7 31.9 - - + -
616A ILE* 3.7 17.5 - - + -
627A THR 3.6 14.1 - - - +
628A ILE* 3.1 20.9 + - + +
630A LYS* 1.3 78.5 - - - +
632A CYS* 1.3 57.5 + - - +
634A VAL* 3.3 5.2 + - + +
635A LEU* 2.9 47.4 + - + +
8B ILE* 3.8 18.8 - - + -
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Residues in contact with CYS 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PHE* 5.1 9.6 - - - -
441A PHE* 3.7 39.1 - - + -
444A GLU* 5.1 7.4 - - + -
445A VAL* 4.0 7.8 - - + +
583A SER* 5.0 0.2 - - - -
587A VAL* 4.1 26.5 - - - -
607A PHE* 5.4 1.8 - - - -
628A ILE* 3.0 26.1 + - - +
629A GLY* 3.2 10.7 + - - +
631A VAL* 1.3 76.6 - - - +
633A ARG* 1.3 62.9 + - + +
635A LEU* 3.4 2.2 + - - +
636A LEU* 3.0 23.9 + - - +
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Residues in contact with ARG 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ALA 4.7 0.3 - - - +
410A SER* 3.0 30.7 + - - +
411A GLU* 5.2 1.0 - - - +
412A LEU* 3.7 48.4 - - - +
444A GLU* 3.7 24.6 + - - +
445A VAL* 4.3 9.9 - - - -
448A CYS* 3.9 20.3 - - + -
629A GLY* 3.0 27.9 + - - +
630A LYS* 3.6 30.7 - - - +
632A CYS* 1.3 75.5 - - - +
634A VAL* 1.3 57.1 + - - +
636A LEU* 3.4 2.9 + - - +
637A ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A PHE* 3.8 2.6 - - + -
410A SER* 4.0 20.2 - - - +
616A ILE* 4.9 11.4 - - + -
630A LYS* 2.9 34.5 + - + +
631A VAL* 3.8 5.6 - - + +
633A ARG* 1.3 77.7 - - - +
635A LEU* 1.3 61.2 + - + +
637A ALA* 3.2 2.6 + - - +
638A LYS* 2.9 27.0 + - - +
3B VAL* 3.7 27.8 - - + -
5B PRO* 3.7 34.8 - - + -
8B ILE* 6.0 2.0 - - + -
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Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A SER* 4.0 11.3 - - - -
586A GLN* 3.7 32.9 - - + +
587A VAL* 3.9 25.8 - - + -
590A MET* 4.9 7.6 - - + -
631A VAL* 2.9 30.2 + - + +
632A CYS* 4.0 3.8 - - - +
634A VAL* 1.3 77.2 - - + +
636A LEU* 1.3 60.5 + - - +
638A LYS* 3.3 18.6 + - + +
639A SER* 3.0 29.1 + - - -
5B PRO* 4.7 11.0 - - + +
8B ILE* 5.3 11.2 - - + -
20B THR* 4.4 16.2 - - + -
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Residues in contact with LEU 636 (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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441A PHE* 5.1 0.2 - - + -
445A VAL* 3.7 24.7 - - + +
448A CYS* 5.0 3.4 - - - -
450A ALA* 3.8 20.2 - - + -
451A SER* 3.8 22.4 - - - +
454A ILE* 4.4 6.5 - - + -
579A CYS* 3.9 9.9 - - + +
580A LEU* 3.8 43.5 - - + +
583A SER* 3.9 11.8 - - - +
632A CYS 3.0 17.8 + - - +
633A ARG 3.8 3.4 - - - +
635A LEU* 1.3 77.5 - - - +
637A ALA* 1.3 56.6 + - - +
639A SER* 3.3 3.5 + - - -
640A VAL* 2.9 29.4 + - + +
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Residues in contact with ALA 637 (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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406A PHE* 3.5 13.6 - - + -
409A ALA* 3.3 30.5 - - + +
410A SER* 3.3 17.0 - - - +
450A ALA* 4.1 9.8 - - - +
633A ARG 2.9 11.7 + - - +
634A VAL 3.2 3.6 + - - +
636A LEU* 1.3 75.7 - - - +
638A LYS* 1.3 56.5 + - - +
640A VAL* 4.4 1.3 - - - -
641A PHE* 2.9 35.4 + - - +
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Residues in contact with LYS 638 (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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406A PHE* 3.6 11.4 - - + -
634A VAL 2.9 17.2 + - - +
635A LEU* 3.6 15.9 - - + +
636A LEU 3.2 0.4 - - - -
637A ALA* 1.3 76.4 - - - +
639A SER* 1.3 57.4 + - - +
641A PHE 3.5 1.1 + - - +
642A ASN* 2.9 43.8 + - - +
694A TRP* 4.2 13.4 - - + -
698A ASN* 4.7 14.4 - - - -
701A TRP* 5.0 5.2 - - + -
5B PRO* 3.8 33.7 - - + +
6B MET* 4.5 18.2 - - - +
9B PHE* 5.9 0.4 - - - -
20B THR* 3.7 38.4 + - - +
21B THR* 5.5 1.6 - - - +
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Residues in contact with SER 639 (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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579A CYS* 3.3 34.3 - - - -
582A GLN* 2.8 30.4 + - - +
583A SER* 4.4 2.1 + - - -
586A GLN* 4.1 8.5 + - - -
635A LEU 3.0 17.6 + - - -
636A LEU* 3.3 4.2 + - - -
638A LYS* 1.3 72.6 - - - +
640A VAL* 1.3 65.8 + - - +
642A ASN* 3.3 7.3 + - - +
643A SER 3.0 17.0 + - - -
25B THR* 3.4 5.6 + - - -
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Residues in contact with VAL 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ALA* 3.9 15.5 - - + +
453A TYR* 4.2 20.2 - - + -
454A ILE* 3.7 33.7 - - + -
576A MET* 4.7 5.6 - - + -
579A CYS* 3.9 11.4 - - + -
636A LEU* 2.9 22.6 + - + +
637A ALA* 3.8 4.7 - - - +
639A SER* 1.3 75.8 - - - +
641A PHE* 1.3 65.3 + - + +
643A SER* 2.9 4.9 + - - -
644A ILE* 2.9 47.5 + - + +
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Residues in contact with PHE 641 (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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284A LEU* 3.7 19.5 - - + -
402A ILE* 3.9 20.2 - - + -
405A GLU* 4.0 26.2 - - + -
406A PHE* 4.3 7.4 - + - -
409A ALA* 3.6 23.3 - - + -
450A ALA* 6.4 0.2 - - + -
453A TYR* 4.2 15.3 - + - -
637A ALA 2.9 22.5 + - - +
640A VAL* 1.3 83.5 - - + +
642A ASN* 1.3 62.0 + - - +
644A ILE* 4.3 7.2 - - + +
645A TYR* 3.4 48.5 + + - +
694A TRP* 3.7 40.6 + + + -
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Residues in contact with ASN 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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638A LYS* 2.9 30.1 + - - +
639A SER* 3.6 8.3 + - - +
640A VAL 3.2 0.2 - - - -
641A PHE* 1.3 77.6 - - - +
643A SER* 1.3 58.5 + - - +
644A ILE 3.5 0.2 - - - -
646A ALA* 3.3 25.7 - - - +
650A LEU* 3.7 10.8 - - - +
694A TRP* 2.4 39.7 + - - +
698A ASN* 5.3 1.2 - - - +
20B THR 5.0 7.9 + - - -
22B PHE 5.0 0.6 + - - -
23B PRO* 3.4 37.7 - - + +
25B THR* 4.2 9.9 - - - +
26B GLY 4.2 3.5 + - - -
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Residues in contact with SER 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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572A TRP 4.5 5.4 + - - -
576A MET* 3.5 26.1 - - - +
579A CYS* 3.9 12.6 - - - -
639A SER 3.0 11.5 + - - -
640A VAL 2.9 8.9 + - - -
642A ASN* 1.3 77.7 - - - +
644A ILE* 1.3 63.6 + - - +
646A ALA* 4.2 8.0 - - - +
25B THR 3.0 25.4 + - - -
26B GLY* 3.9 10.9 - - - +
27B ASP* 5.1 2.3 - - - +
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Residues in contact with ILE 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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279A ARG* 4.5 11.3 + - - +
280A SER* 4.1 21.0 - - - -
281A LYS* 5.4 1.8 - - + +
282A PHE* 4.3 16.8 - - + -
284A LEU* 4.1 26.2 - - + -
453A TYR* 4.6 6.1 - - + -
576A MET* 4.2 19.7 - - + -
640A VAL* 2.9 34.6 + - + +
641A PHE* 4.5 5.8 - - + -
642A ASN 3.5 0.2 - - - -
643A SER* 1.3 80.6 - - - +
645A TYR* 1.3 80.9 + - + +
646A ALA 3.3 4.2 + - - +
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Residues in contact with TYR 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLN* 2.7 28.9 + - - -
279A ARG* 3.6 50.0 + - + +
280A SER* 4.4 4.7 - - - -
284A LEU* 4.0 7.3 - - + +
401A TRP* 3.8 13.0 - + - -
402A ILE* 4.4 7.1 - - + +
641A PHE* 3.4 48.5 + + - +
642A ASN 4.4 0.4 - - - -
644A ILE* 1.3 91.7 - - + +
646A ALA* 1.3 61.8 + - - +
647A SER 3.5 1.0 + - - -
650A LEU* 4.5 8.7 - - - +
692A ASP* 3.2 16.2 - - - +
693A PRO* 4.5 20.2 - - + -
694A TRP* 3.7 21.0 - - + +
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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