Contacts of the helix formed by residues 633 - 645 (chain A) in PDB entry 5E2Q
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 633 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A SER* 5.0 12.0 + - - -
499A PHE* 3.7 4.6 - - - -
628A LEU* 2.9 29.9 + - + +
631A THR* 3.1 18.2 - - - +
632A GLY* 1.3 72.6 - - - +
634A VAL* 1.3 51.3 + - - +
635A ALA* 3.6 8.5 + - - +
636A GLY* 3.0 20.2 + - - -
637A GLY* 2.7 33.4 + - - -
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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
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498A LYS* 3.4 41.7 - - - +
499A PHE* 3.8 22.4 - - + -
632A GLY 2.7 10.9 + - - +
633A ASP* 1.3 67.9 - - - +
635A ALA* 1.3 62.1 + - + +
638A ARG* 2.7 67.3 + - + +
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Residues in contact with ALA 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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633A ASP* 3.3 6.2 + - - +
634A VAL* 1.3 85.4 - - + +
636A GLY* 1.3 57.1 + - - +
638A ARG* 3.6 5.0 + - - +
639A ALA* 3.0 27.9 + - - +
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Residues in contact with GLY 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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624A ARG* 5.4 0.2 + - - -
628A LEU* 3.4 13.4 - - - +
633A ASP* 3.0 23.1 + - - -
635A ALA* 1.3 73.9 - - - +
637A GLY* 1.3 60.3 + - - +
639A ALA* 3.3 7.1 + - - +
640A LEU* 2.8 32.7 + - - +
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Residues in contact with GLY 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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499A PHE* 4.0 13.9 - - - -
502A ILE* 4.3 7.0 - - - -
506A TYR* 3.8 7.9 - - - -
628A LEU* 3.7 13.3 - - - +
633A ASP 2.7 21.3 + - - -
634A VAL 3.7 1.3 - - - -
635A ALA 3.3 0.2 - - - -
636A GLY* 1.3 73.2 - - - +
638A ARG* 1.3 55.5 + - - +
640A LEU* 3.4 1.4 + - - +
641A TYR* 2.9 33.6 + - - +
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Residues in contact with ARG 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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498A LYS 4.5 1.4 + - - -
499A PHE 3.2 11.4 + - - -
500A SER* 2.7 22.4 + - - -
501A THR* 2.5 29.9 + - - -
502A ILE* 3.6 21.2 - - + +
634A VAL* 2.7 47.5 + - + +
635A ALA* 4.0 4.9 - - - +
637A GLY* 1.3 69.2 - - - +
639A ALA* 1.3 64.5 + - - +
642A GLU* 3.0 59.0 + - - +
643A GLY 4.2 0.2 + - - -
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Residues in contact with ALA 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 ALA 3.0 19.3 + - - +
636A GLY* 3.3 9.2 + - - +
638A ARG* 1.3 77.0 - - - +
640A LEU* 1.3 61.1 + - - +
643A GLY* 3.7 13.5 + - - -
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Residues in contact with LEU 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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506A TYR* 4.4 2.2 - - + +
621A PHE* 4.6 10.8 - - + -
624A ARG* 3.8 45.3 - - + +
625A LEU* 3.9 24.2 - - + -
628A LEU* 3.8 17.5 - - + -
636A GLY 2.8 16.8 + - - +
637A GLY 3.8 2.5 - - - +
639A ALA* 1.3 79.2 - - - +
641A TYR* 1.3 65.1 + - - +
643A GLY* 3.6 6.4 + - - -
644A TYR* 3.4 40.9 + - + +
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Residues in contact with TYR 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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502A ILE* 4.6 18.6 - - + -
505A SER* 2.5 40.9 + - - -
506A TYR* 3.7 30.7 - + + -
509A CYS* 3.5 31.6 - - + -
570A GLN* 3.3 28.9 - - + -
571A ALA* 3.3 17.0 + - - -
574A VAL* 3.8 16.7 - - + +
621A PHE* 5.1 1.3 - + - -
625A LEU* 4.7 6.5 - - + -
637A GLY 2.9 21.4 + - - +
640A LEU* 1.3 72.6 - - - +
642A GLU* 1.3 58.3 + - + +
643A GLY 3.0 4.4 + - - -
644A TYR* 3.3 6.0 + - - +
645A ALA* 3.0 27.9 + - - +
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Residues in contact with GLU 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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501A THR* 5.2 0.7 + - - -
502A ILE* 3.5 28.4 - - + +
570A GLN* 5.8 2.2 - - - +
638A ARG* 3.0 47.7 + - - +
641A TYR* 1.3 76.9 - - + +
643A GLY* 1.3 51.2 + - - +
645A ALA* 3.8 9.9 - - + -
646A THR* 2.7 31.5 + - - -
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Residues in contact with GLY 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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577A ARG* 3.3 13.2 + - - -
639A ALA 3.7 13.1 + - - -
640A LEU 3.6 6.9 + - - -
641A TYR 3.0 1.2 - - - -
642A GLU* 1.3 78.7 - - - +
644A TYR* 1.3 61.7 + - - +
646A THR* 3.1 17.9 + - - -
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Residues in contact with TYR 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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573A PHE* 3.5 3.6 - - - -
574A VAL* 3.7 21.9 - - + +
577A ARG* 3.3 53.1 + - + +
578A VAL* 4.0 22.8 - - + +
581A GLU* 2.5 46.1 + - + -
621A PHE* 4.1 26.0 - + - +
640A LEU* 3.4 43.4 + - + +
641A TYR* 3.3 3.6 + - - +
643A GLY* 1.3 72.9 - - - +
645A ALA* 1.3 57.3 + - - +
646A THR 3.1 6.6 + - - -
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Residues in contact with ALA 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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557A TYR* 4.8 1.0 - - - -
564A TRP* 3.0 24.9 + - + +
570A GLN* 3.5 29.2 - - + +
573A PHE* 4.2 7.6 - - - -
574A VAL* 3.9 15.2 - - + +
641A TYR 3.0 18.3 + - - +
642A GLU* 4.0 9.4 - - - -
643A GLY 3.2 0.8 - - - -
644A TYR* 1.3 75.5 - - - +
646A THR* 1.3 61.9 + - - +
647A VAL* 3.4 3.3 + - - +
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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