Contacts of the helix formed by residues 636 - 647 (chain A) in PDB entry 2P2B
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 GLY 636 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A ASP* 3.0 13.9 + - - -
635A PRO* 1.3 80.0 - - - +
637A VAL* 1.3 61.7 + - - +
638A VAL 3.3 1.0 + - - -
639A GLU* 3.4 17.2 + - - +
640A LYS* 3.5 10.9 + - - +
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Residues in contact with VAL 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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600A ASP 5.3 0.2 - - - +
601A SER* 3.3 39.4 - - - +
602A LEU 4.2 6.5 - - - +
603A PRO* 3.7 32.5 - - + -
634A ASP* 3.2 35.9 - - + +
635A PRO* 3.1 2.4 - - + -
636A GLY* 1.3 77.3 - - - +
638A VAL* 1.3 67.1 + - + +
640A LYS* 3.3 3.8 + - - +
641A LEU* 2.8 33.9 + - + +
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Residues in contact with VAL 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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603A PRO* 5.5 1.3 - - + -
614A ILE* 4.2 36.8 - - + -
618A ILE* 4.3 8.5 - - + -
635A PRO* 3.5 14.3 + - + +
636A GLY 3.3 1.0 - - - -
637A VAL* 1.3 84.6 - - + +
639A GLU* 1.3 56.5 + - - +
641A LEU* 3.4 10.0 + - + +
642A LEU* 2.9 50.4 + - + +
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Residues in contact with GLU 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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635A PRO 4.6 0.8 + - - -
636A GLY* 3.4 12.3 + - - +
637A VAL 3.3 0.6 - - - -
638A VAL* 1.3 75.2 - - - +
640A LYS* 1.3 66.8 + - - +
642A LEU* 3.3 30.0 + - - +
643A GLU* 3.3 19.1 + - - +
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Residues in contact with LYS 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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601A SER* 3.7 23.1 - - - +
636A GLY 3.5 7.7 + - - +
637A VAL* 3.3 5.5 + - - +
639A GLU* 1.3 78.7 - - - +
641A LEU* 1.3 57.8 + - - +
643A GLU* 3.3 5.0 + - - +
644A GLU* 3.0 40.7 + - + +
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Residues in contact with LEU 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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562A TYR* 3.7 34.1 - - + -
597A HIS* 3.8 4.0 - - - +
599A THR* 3.8 16.2 - - + +
601A SER* 3.3 29.2 - - - +
602A LEU* 5.4 0.2 - - - -
603A PRO* 3.8 20.0 - - + -
614A ILE* 5.6 0.2 - - + -
615A LEU* 4.0 8.7 - - + -
618A ILE* 3.8 22.8 - - + +
637A VAL* 2.8 31.4 + - + +
638A VAL* 3.6 7.9 - - + +
640A LYS* 1.3 71.5 - - - +
642A LEU* 1.3 58.2 + - - +
644A GLU* 3.7 9.2 + - - +
645A LYS* 3.0 30.5 + - - +
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Residues in contact with LEU 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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618A ILE* 4.1 28.9 - - + -
638A VAL* 2.9 39.6 + - + +
639A GLU* 3.3 28.2 + - - +
641A LEU* 1.3 76.8 - - - +
643A GLU* 1.3 60.6 + - - +
645A LYS* 3.5 4.3 + - - +
646A GLN* 3.2 22.4 + - - +
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Residues in contact with GLU 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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639A GLU* 3.3 15.0 + - - +
640A LYS* 3.9 7.2 - - - +
642A LEU* 1.3 75.8 - - - +
644A GLU* 1.3 65.1 + - + +
646A GLN* 3.3 9.4 + - - +
647A ALA* 3.2 23.0 + - - +
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Residues in contact with GLU 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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597A HIS* 2.7 40.3 + - + +
598A TRP 3.9 10.3 - - - +
599A THR* 2.9 29.4 + - - -
600A ASP 4.4 2.8 + - - -
601A SER* 4.6 1.9 + - - -
640A LYS* 3.0 29.8 + - - +
641A LEU* 3.7 8.5 - - - +
643A GLU* 1.3 75.0 - - - +
645A LYS* 1.3 63.0 + - - +
647A ALA* 3.3 21.5 + - - +
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Residues in contact with LYS 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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560A TYR* 3.6 24.0 - - - +
597A HIS* 3.6 7.6 - - + +
618A ILE* 3.6 31.4 + - + +
619A ALA* 3.4 27.8 + - - +
620A ALA 4.7 1.4 + - - -
621A GLY* 4.4 11.4 - - - +
641A LEU 3.0 18.3 + - - +
642A LEU* 3.6 6.1 - - - +
644A GLU* 1.3 75.9 - - - +
646A GLN* 1.3 63.8 + - - +
647A ALA 3.2 9.2 + - - +
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Residues in contact with GLN 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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642A LEU 3.2 11.3 + - - +
643A GLU* 3.3 11.6 + - - +
645A LYS* 1.3 81.4 - - - +
647A ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 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 GLU 3.2 13.9 + - - +
644A GLU* 3.7 14.8 - - - +
645A LYS 3.1 8.5 - - - +
646A GLN* 1.3 81.6 - - - +
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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