Contacts of the helix formed by residues 633 - 649 (chain A) in PDB entry 2A8B
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 633 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A PHE* 3.4 17.5 - - - -
631A VAL* 4.1 0.5 - - - +
632A GLN* 1.3 89.0 - - + +
634A SER* 1.3 59.2 + - - +
635A GLU* 3.6 11.6 + - - +
636A GLN* 3.2 36.1 + - - +
637A TYR 3.2 19.6 + - - -
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Residues in contact with SER 634 (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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393A LEU 4.8 0.6 - - - +
394A GLN* 3.8 31.4 - - - +
397A PHE* 3.4 36.6 - - - -
633A THR* 1.3 72.1 - - - +
635A GLU* 1.3 61.4 + - - +
637A TYR* 3.2 3.4 + - - +
638A GLU* 2.9 37.5 + - - +
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Residues in contact with GLU 635 (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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555A HIS 3.3 22.7 - - - +
556A LYS* 3.5 12.7 - - - +
557A THR* 3.5 32.2 + - + +
633A THR* 3.6 10.0 + - - +
634A SER* 1.3 82.4 + - - +
636A GLN* 1.3 56.3 + - - +
638A GLU* 3.4 11.8 + - + +
639A PHE* 2.9 27.4 + - - +
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Residues in contact with GLN 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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552A TRP* 4.5 6.6 - - + +
557A THR* 3.8 17.6 - - + +
593A GLY* 3.3 27.0 - - - +
594A ARG* 4.1 9.5 - - - +
597A CYS* 3.4 20.5 - - - -
631A VAL* 3.9 6.7 - - + -
632A GLN* 2.8 33.4 + - - +
633A THR* 3.2 27.6 + - - +
634A SER 3.2 0.2 - - - -
635A GLU* 1.3 75.5 - - - +
637A TYR* 1.3 59.6 + - - +
639A PHE* 3.0 4.0 + - - +
640A VAL* 2.8 32.2 + - - +
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Residues in contact with TYR 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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393A LEU* 3.6 34.1 - - + -
396A GLU* 2.5 31.4 + - - +
397A PHE* 3.6 34.1 - + + -
400A ILE* 4.2 13.2 - - + -
616A ALA* 4.1 5.8 - - + -
617A LEU* 3.2 22.3 + - - +
620A VAL* 3.7 30.7 - - + -
631A VAL* 3.6 7.9 - - + +
633A THR 3.2 3.6 + - - +
634A SER 3.3 9.2 - - - +
636A GLN* 1.3 77.4 - - - +
638A GLU* 1.3 54.5 + - - +
640A VAL* 3.4 8.2 + - + +
641A HIS* 2.7 54.0 + + - -
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Residues in contact with GLU 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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387A VAL 4.8 5.4 - - - +
390A SER* 2.6 47.7 + - - +
393A LEU* 3.8 31.4 - - + +
394A GLN* 5.1 2.8 + - - +
634A SER* 2.9 23.0 + - - +
635A GLU* 3.6 12.9 - - + +
637A TYR* 1.3 71.6 - - - +
639A PHE* 1.3 59.4 + - - +
641A HIS* 2.9 18.7 + - - +
642A HIS* 2.9 32.7 + - + +
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Residues in contact with PHE 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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552A TRP* 3.7 32.5 - + - -
557A THR* 3.7 18.2 - - + +
558A PRO* 3.4 44.2 - - + -
559A ASP 5.2 0.2 - - - -
560A SER 3.9 2.5 - - - -
561A ALA* 3.8 35.2 - - + -
564A LEU* 3.8 25.8 - - + -
597A CYS* 4.6 6.3 - - + -
635A GLU 2.9 15.2 + - - +
636A GLN 3.3 7.2 - - - +
638A GLU* 1.3 75.2 - - - +
640A VAL* 1.3 66.6 + - - +
642A HIS* 3.3 19.8 + + + +
643A ALA* 3.1 20.5 + - + +
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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
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597A CYS* 3.8 33.4 - - + +
600A ALA* 4.2 15.3 - - + +
601A THR* 3.6 27.8 - - - +
616A ALA* 5.3 5.6 - - + -
620A VAL* 5.9 2.0 - - + -
631A VAL* 4.7 4.9 - - + -
636A GLN 2.8 18.6 + - - +
637A TYR* 3.5 13.0 - - + +
638A GLU 3.2 0.2 - - - -
639A PHE* 1.3 77.6 - - + +
641A HIS* 1.3 60.2 + - + +
643A ALA* 3.1 3.7 + - - +
644A LEU* 2.9 45.9 + - + +
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Residues in contact with HIS 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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378A LEU* 4.2 15.2 - - + +
383A LEU* 4.1 8.7 - - + +
386A VAL* 3.6 26.7 - - + -
387A VAL* 4.2 11.4 - - + -
393A LEU* 3.7 23.0 - - + +
396A GLU* 4.5 3.2 + - - -
616A ALA* 3.7 25.0 - - + +
637A TYR* 2.7 57.9 + + - -
638A GLU 2.9 9.2 + - - +
640A VAL* 1.3 76.2 - - + +
642A HIS* 1.3 54.9 + - + +
644A LEU* 3.7 7.1 - - + +
645A CYS* 2.8 37.8 + - - +
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Residues in contact with HIS 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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387A VAL* 3.4 44.8 - - + +
557A THR* 6.0 0.4 - - - -
558A PRO 5.9 0.7 - - - -
559A ASP 5.9 2.0 - - - -
561A ALA* 4.1 12.4 - - + +
638A GLU* 2.9 34.1 + - + +
639A PHE* 3.4 25.1 - + + +
641A HIS* 1.3 74.9 - - - +
643A ALA* 1.3 57.2 + - - +
645A CYS* 3.4 2.5 + - - +
646A LEU* 2.9 28.6 + - - +
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Residues in contact with ALA 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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561A ALA* 3.7 20.4 - - + +
564A LEU* 5.1 8.1 - - + -
565A LEU* 4.1 10.5 - - + +
601A THR* 3.6 28.7 - - + +
639A PHE* 3.1 13.6 + - + +
640A VAL 3.5 7.6 - - - +
642A HIS* 1.3 73.9 - - - +
644A LEU* 1.3 60.9 + - - +
646A LEU* 3.1 6.3 + - - +
647A TYR* 2.9 29.2 + - - +
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Residues in contact with LEU 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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383A LEU* 4.0 11.9 - - + -
600A ALA 4.6 0.7 - - - +
601A THR* 3.7 16.6 - - - +
604A GLY* 3.5 12.6 - - - +
605A CYS* 3.5 33.9 - - - +
608A LEU* 3.2 22.2 - - + +
614A VAL* 3.9 24.7 - - + -
616A ALA* 4.2 15.7 - - + -
619A ILE* 5.9 0.4 - - + -
640A VAL* 2.9 35.1 + - + +
641A HIS* 3.8 8.3 - - + +
643A ALA* 1.3 74.9 - - - +
645A CYS* 1.3 57.3 + - - +
647A TYR* 3.4 3.4 + - - +
648A GLU* 3.0 23.0 + - - +
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Residues in contact with CYS 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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383A LEU* 3.4 36.5 - - - +
384A ARG* 3.7 20.9 - - + +
387A VAL* 3.4 25.1 - - + -
641A HIS 2.8 18.1 + - - +
642A HIS* 3.5 6.1 - - - +
644A LEU* 1.3 71.7 - - - +
646A LEU* 1.3 65.0 + - - +
648A GLU* 3.1 17.0 + - - +
649A SER* 3.2 13.9 + - - -
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Residues in contact with LEU 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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560A SER* 5.2 1.3 - - - +
561A ALA* 3.7 11.7 - - + +
562A GLN* 3.3 44.2 - - + +
565A LEU* 3.8 14.4 - - + -
642A HIS 2.9 17.6 + - - +
643A ALA 3.4 5.4 - - - +
645A CYS* 1.3 75.2 - - - +
647A TYR* 1.3 59.5 + - - +
649A SER* 2.7 26.8 + - - +
650A ARG* 3.6 17.0 + - - +
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Residues in contact with TYR 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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565A LEU* 3.7 20.1 - - + +
568A MET* 4.3 3.8 - - + -
569A LEU* 3.9 25.4 - - + -
572A GLU* 4.5 11.4 + - - -
605A CYS* 3.2 59.4 + - + -
608A LEU* 3.8 16.8 - - + -
609A LYS* 3.7 21.5 - - - +
643A ALA 2.9 9.6 + - - +
644A LEU 3.5 6.5 - - - +
645A CYS 3.2 0.2 - - - -
646A LEU* 1.3 77.6 - - - +
648A GLU* 1.3 64.7 + - - +
650A ARG* 3.1 24.8 + - + +
651A LEU* 3.6 28.2 + - + +
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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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380A ARG* 3.4 50.2 + - + +
383A LEU* 4.1 11.7 - - + -
384A ARG* 3.2 50.1 + - - +
608A LEU* 4.3 4.5 - - + -
644A LEU 3.0 17.8 + - - +
645A CYS 3.1 7.1 + - - +
647A TYR* 1.3 77.6 - - - +
649A SER* 1.3 68.1 + - - +
651A LEU* 3.0 29.8 + - + +
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Residues in contact with SER 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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384A ARG* 6.1 1.6 - - - -
645A CYS 3.2 9.7 + - - -
646A LEU* 2.7 29.9 + - - +
648A GLU* 1.3 83.0 + - - +
650A ARG* 1.3 62.0 + - - +
651A LEU 3.4 4.3 - - - +
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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
------------------------------------------------------------
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