Contacts of the helix formed by residues 472 - 480 (chain A) in PDB entry 4LTS
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 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A TYR 3.4 10.8 - - - -
232A GLY* 3.7 10.1 - - - -
471A TYR* 1.3 76.9 - - - +
473A PHE* 1.3 64.2 + - - +
474A ASP* 3.4 11.8 + - - +
475A GLU* 2.8 39.2 + - - +
476A ILE* 3.1 23.1 + - - +
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Residues in contact with PHE 473 (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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60A TYR* 3.7 30.7 - + - -
209A SER 3.3 21.8 - - - -
212A LEU 3.5 17.5 - - - -
213A VAL* 3.6 17.5 - - + -
227A ILE* 3.5 37.0 - - + -
231A TYR* 3.9 19.9 - + + +
232A GLY 2.8 19.7 + - - +
233A THR* 3.5 18.8 - - + -
238A PRO* 4.3 1.1 - - + -
472A SER* 1.3 72.0 - - - +
474A ASP* 1.3 57.2 + - - +
476A ILE* 3.3 7.0 + - + +
477A ARG* 2.9 52.0 + - + +
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Residues in contact with ASP 474 (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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233A THR* 3.6 21.9 - - - +
234A LYS* 2.8 36.5 + - - +
235A ASP* 5.2 1.4 + - - +
472A SER* 3.1 9.6 + - - +
473A PHE* 1.3 78.2 - - - +
475A GLU* 1.3 61.8 + - - +
477A ARG* 3.4 15.2 + - - +
478A LYS* 3.1 21.5 + - - +
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Residues in contact with GLU 475 (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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470A SER 4.2 3.7 - - - +
471A TYR* 3.5 28.2 - - + -
472A SER* 2.8 39.2 + - - +
474A ASP* 1.3 76.3 - - + +
476A ILE* 1.3 57.7 + - - +
478A LYS* 3.2 15.4 + - - +
479A ASN* 3.0 36.2 + - - +
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Residues in contact with ILE 476 (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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60A TYR* 4.0 21.8 - - + -
121A GLU* 3.6 36.1 - - + +
122A GLY* 3.5 17.6 - - - +
213A VAL* 4.1 18.2 - - + -
231A TYR* 3.4 41.1 - - + -
471A TYR* 4.0 9.6 - - + -
472A SER 3.1 12.4 + - - +
473A PHE* 3.6 11.2 - - + +
475A GLU* 1.3 76.7 - - - +
477A ARG* 1.3 63.0 + - - +
479A ASN 3.2 1.4 + - - -
480A ALA* 3.0 22.2 + - - +
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Residues in contact with ARG 477 (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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212A LEU* 2.9 27.9 + - - +
213A VAL* 3.5 25.7 - - - +
215A PHE 3.4 11.9 + - - -
216A LYS* 3.9 19.0 - - - +
233A THR* 4.8 6.1 - - - +
235A ASP* 5.8 1.6 + - - -
238A PRO* 2.7 39.0 + - - +
473A PHE* 2.9 39.2 + - + +
474A ASP* 3.6 13.0 + - - +
476A ILE* 1.3 77.6 - - - +
478A LYS* 1.3 61.9 + - - +
480A ALA* 3.2 11.4 + - - +
481A GLN* 3.3 15.7 + - - +
603A EDO 3.5 23.3 + - - +
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Residues in contact with LYS 478 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A ASP 3.1 14.2 + - - +
475A GLU* 3.2 15.1 + - - +
477A ARG* 1.3 76.3 - - - +
479A ASN* 1.3 82.5 + - - +
480A ALA 3.3 0.3 + - - -
481A GLN* 3.2 39.8 + - - +
486A LEU* 5.9 0.5 - - - +
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Residues in contact with ASN 479 (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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120A PRO* 4.4 4.9 - - - +
121A GLU 2.9 20.2 + - - -
122A GLY* 3.2 20.9 - - - +
123A PHE* 3.7 28.9 - - + +
124A VAL* 4.0 2.1 - - - +
471A TYR* 5.1 3.8 - - - -
475A GLU* 3.0 22.4 + - - +
476A ILE 3.2 4.7 + - - +
478A LYS* 1.3 95.3 + - - +
480A ALA* 1.3 60.1 + - - +
481A GLN 3.6 2.6 + - - +
604A EDO 2.9 31.5 + - - -
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Residues in contact with ALA 480 (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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58A VAL* 4.2 10.1 - - + -
122A GLY 3.4 12.1 - - - +
124A VAL* 4.0 6.3 - - + -
166A ARG* 2.8 28.7 + - - +
169A LYS* 5.7 1.6 + - - -
213A VAL* 3.5 27.4 - - + +
214A ASN* 4.4 7.8 + - - +
476A ILE 3.0 15.3 + - - +
477A ARG 3.2 4.4 + - - +
478A LYS 3.2 0.8 - - - -
479A ASN* 1.3 76.2 - - - +
481A GLN* 1.3 59.9 + - - +
482A LEU* 4.9 0.5 - - - +
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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