Contacts of the helix formed by residues 494 - 504 (chain A) in PDB entry 3S1M
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 SER 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A TYR* 3.6 5.7 - - - -
492A PRO* 4.3 0.5 - - - +
493A GLN* 1.3 79.7 - - - +
495A GLU* 1.4 59.4 + - - +
496A GLU* 2.8 36.7 + - - +
497A THR* 3.2 17.9 + - - -
498A ARG* 3.0 30.7 + - - +
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Residues in contact with GLU 495 (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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376A TYR* 3.5 20.8 + - - +
378A GLU* 6.1 0.7 - - - +
494A SER* 1.4 72.8 + - - +
496A GLU* 1.3 60.4 + - - +
498A ARG* 3.2 20.0 + - - +
499A ALA* 2.9 27.3 + - - +
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Residues in contact with GLU 496 (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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494A SER* 2.8 21.3 + - - +
495A GLU* 1.3 78.7 + - - +
497A THR* 1.3 60.7 + - - +
499A ALA* 3.3 10.0 + - - +
500A GLU* 3.0 33.4 + - + +
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Residues in contact with THR 497 (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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492A PRO* 3.4 23.1 - - + -
493A GLN 4.7 0.9 - - - +
494A SER* 3.2 28.2 + - - -
495A GLU 3.3 0.2 - - - -
496A GLU* 1.3 80.8 - - - +
498A ARG* 1.4 60.2 + - - +
500A GLU* 3.3 24.3 + - - +
501A LEU* 3.3 17.8 + - + +
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Residues in contact with ARG 498 (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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376A TYR* 3.6 39.0 - - + +
434A ARG* 3.5 12.0 - - - +
436A ILE* 5.7 0.6 - - - +
439A ASN 5.5 0.2 + - - -
440A ASP* 2.8 35.8 + - - +
441A PRO* 3.4 37.9 + - + +
491A VAL* 6.3 0.4 - - - +
492A PRO* 3.5 24.2 - - + +
494A SER 3.0 21.3 + - - +
495A GLU* 3.4 27.5 + - - +
497A THR* 1.4 74.8 - - - +
499A ALA* 1.4 62.0 + - - +
501A LEU* 3.5 2.3 + - - +
502A SER* 3.2 21.5 + - - -
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Residues in contact with ALA 499 (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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495A GLU 2.9 12.7 + - - +
496A GLU* 3.4 14.1 - - - +
497A THR 3.3 0.2 - - - -
498A ARG* 1.4 72.8 - - - +
500A GLU* 1.4 56.2 + - - +
502A SER* 3.0 9.3 + - - -
503A GLN* 2.8 45.8 + - + +
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Residues in contact with GLU 500 (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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496A GLU* 3.0 18.5 + - + +
497A THR* 3.4 18.2 - - - +
499A ALA* 1.4 74.5 - - - +
501A LEU* 1.3 60.2 + - + +
503A GLN* 5.1 0.4 - - - -
504A LEU* 3.2 47.2 + - + +
505A CYS* 3.6 6.6 + - - -
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Residues in contact with LEU 501 (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 PRO* 4.1 13.0 - - + +
442A VAL 4.1 1.1 - - - -
443A LEU* 3.8 50.3 - - + +
457A ALA* 3.6 11.9 - - + -
492A PRO* 3.8 34.5 - - + -
497A THR* 3.3 14.8 + - + +
498A ARG 3.8 6.3 - - - +
499A ALA 3.2 0.6 - - - -
500A GLU* 1.3 79.0 - - + +
502A SER* 1.3 56.2 + - - +
505A CYS* 3.0 22.1 + - + -
506A ALA 2.8 31.0 + - - -
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Residues in contact with SER 502 (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 PRO* 4.6 11.4 - - - +
457A ALA* 4.5 1.8 - - - +
498A ARG 3.2 12.8 + - - -
499A ALA* 3.0 15.4 + - - -
501A LEU* 1.3 79.0 - - - +
503A GLN* 1.3 79.4 + - - +
506A ALA* 3.4 21.8 - - - +
509A LEU* 3.9 3.5 - - - +
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Residues in contact with GLN 503 (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 ALA* 2.8 32.0 + - + +
502A SER* 1.3 102.6 + - - +
504A LEU* 1.3 73.7 + - + +
509A LEU* 3.4 15.2 - - - +
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Residues in contact with LEU 504 (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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500A GLU* 3.2 34.4 + - + +
501A LEU 3.6 0.2 + - - -
503A GLN* 1.3 93.4 - - + +
505A CYS* 1.3 65.8 + - - +
506A ALA 3.5 1.3 - - - -
509A LEU* 3.4 14.2 - - - +
510A GLN* 3.2 19.2 + - - -
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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
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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