Contacts of the helix formed by residues 401 - 409 (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 TRP 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A CYS* 2.9 30.9 + - - -
277A THR 3.6 17.5 - - - -
278A GLN* 3.7 21.1 - - - -
285A MET* 5.1 0.6 - - - +
399A ALA* 3.4 17.6 - - + +
400A SER* 1.3 78.7 - - - +
402A ILE* 1.3 90.2 + - + +
403A GLN 3.2 2.5 - - - -
404A SER* 3.0 10.9 + - - -
405A GLU* 2.9 41.0 + - + +
528A GLU* 3.7 26.0 - - - +
530A HIS* 3.7 15.3 - - - -
531A LYS* 3.7 35.5 - - + +
645A TYR* 3.8 20.4 - - - -
693A PRO* 4.1 21.5 - - + -
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Residues in contact with ILE 402 (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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276A CYS* 5.5 1.1 - - - -
398A LEU* 4.2 18.2 - - + -
399A ALA 4.3 7.0 - - - +
401A TRP* 1.3 108.3 - - + +
403A GLN* 1.3 63.7 + - + +
405A GLU* 4.0 2.9 - - + -
406A PHE* 3.0 27.5 + - - +
641A PHE* 3.9 30.1 - - + -
645A TYR* 4.4 11.2 - - + +
693A PRO* 4.3 19.5 - - + +
694A TRP* 4.4 6.1 - - + -
697A LEU* 3.7 35.3 - - + +
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Residues in contact with GLN 403 (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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400A SER* 4.6 8.7 - - - +
401A TRP 3.2 1.2 - - - +
402A ILE* 1.3 83.5 - - + +
404A SER* 1.3 56.9 + - - +
406A PHE* 3.5 5.1 + - - +
407A ASN* 2.9 40.5 + - - +
697A LEU* 3.7 14.6 - - + +
701A TRP* 2.9 31.4 + - - -
2B ASP* 3.8 31.5 - - - +
3B VAL* 3.2 21.1 + - - +
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Residues in contact with SER 404 (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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285A MET* 4.1 15.5 - - - -
400A SER 3.9 10.9 + - - -
401A TRP* 3.0 14.0 + - - -
403A GLN* 1.3 77.0 - - - +
405A GLU* 1.3 59.9 + - - +
407A ASN* 3.2 11.5 + - - +
408A LYS* 3.0 37.8 + - - +
528A GLU* 5.5 2.1 + - - -
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Residues in contact with GLU 405 (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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278A GLN* 4.1 4.5 + - - -
284A LEU* 3.3 31.5 - - + +
285A MET* 3.3 27.1 + - - +
286A ASP* 4.1 1.0 - - - +
401A TRP* 2.9 38.0 + - + +
402A ILE* 3.3 6.9 + - + +
404A SER* 1.3 76.4 - - - +
406A PHE* 1.3 57.8 + - - +
408A LYS* 3.4 1.6 + - - +
409A ALA* 2.9 30.8 + - - +
453A TYR* 5.0 2.1 + - - -
531A LYS* 2.7 34.1 + - - -
641A PHE* 4.0 20.2 - - + -
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Residues in contact with PHE 406 (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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402A ILE 3.0 16.4 + - - +
403A GLN* 4.0 6.7 - - - +
405A GLU* 1.3 74.6 - - - +
407A ASN* 1.3 66.3 + - - +
409A ALA* 3.8 4.5 + - - -
410A SER* 3.4 15.6 + - - -
634A VAL* 3.8 11.2 - - + -
637A ALA* 3.5 35.9 - - + -
638A LYS* 3.6 14.4 - - - -
641A PHE* 4.3 9.6 - + + -
694A TRP* 3.7 27.8 - + + -
701A TRP* 3.5 31.2 - + + -
3B VAL* 3.7 31.4 - - + +
5B PRO* 3.7 17.9 - - + -
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Residues in contact with ASN 407 (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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403A GLN* 2.9 24.5 + - - +
404A SER* 3.4 13.3 + - - +
405A GLU 3.2 0.2 - - - -
406A PHE* 1.3 77.3 - - - +
408A LYS* 1.3 70.8 + - + +
409A ALA 3.3 1.0 + - - -
410A SER* 3.3 13.9 + - - -
411A GLU* 3.8 15.7 - - - +
630A LYS* 5.1 2.6 + - - -
1B MET 3.3 19.9 + - - -
2B ASP* 3.4 13.0 + - - +
3B VAL* 3.0 37.6 + - - +
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Residues in contact with LYS 408 (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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285A MET* 3.7 38.4 - - + -
404A SER* 3.0 20.0 + - - +
405A GLU 4.2 2.0 - - - +
407A ASN* 1.3 81.1 - - - +
409A ALA* 1.3 55.9 + - - +
410A SER 3.2 5.0 + - - -
411A GLU* 3.9 34.2 + - - +
449A ARG* 3.6 39.4 + - - +
453A TYR* 5.2 2.7 - - - +
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Residues in contact with ALA 409 (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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405A GLU 2.9 18.6 + - - +
406A PHE* 4.3 4.9 - - - +
407A ASN 3.2 1.4 - - - -
408A LYS* 1.3 75.5 - - - +
410A SER* 1.3 58.9 + - - +
411A GLU 3.8 0.7 - - - -
448A CYS* 3.5 14.8 - - - -
449A ARG* 4.3 8.7 - - - -
450A ALA* 3.8 5.3 - - + +
453A TYR* 4.0 15.5 - - + -
637A ALA* 3.3 20.5 - - + +
641A PHE* 3.6 26.7 - - + -
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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