Contacts of the helix formed by residues 194 - 198 (chain B) 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 GLY 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ASP* 2.7 14.9 + - - -
193B PHE* 1.3 76.7 - - - +
195B TYR* 1.3 63.4 + - - +
196B ARG 3.3 2.9 - - - -
197B GLY* 3.0 13.6 + - - -
198B VAL* 3.2 17.2 + - - +
220B THR* 3.9 2.0 + - - -
383B GLY* 3.4 26.3 - - - -
384B GLY 4.6 0.2 - - - -
387B LEU* 4.0 8.5 - - - -
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Residues in contact with TYR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU 3.8 2.4 + - - -
14A ALA* 3.3 19.8 - - - +
15A THR 3.5 39.3 - - - -
16A ASP* 3.3 15.3 - - - +
150A THR* 3.5 8.3 - - + -
154A GLN* 2.8 28.9 + - - -
193B PHE 3.4 3.4 + - - -
194B GLY* 1.3 77.0 - - - +
196B ARG* 1.3 61.0 + - - +
198B VAL* 3.4 6.8 - - - +
201B GLN* 2.7 37.6 + - - -
204B ALA* 3.4 27.6 - - + -
219B ASP 4.0 0.9 - - - -
220B THR* 3.4 29.4 + - + +
221B VAL 3.9 10.8 - - - -
222B ALA* 3.7 17.2 - - + +
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Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 2.8 25.8 + - - -
18A TYR* 3.0 28.5 + - - -
19A LYS* 4.0 6.8 - - - +
149A GLU* 3.4 27.4 + - - -
150A THR* 3.7 23.0 + - + +
153A VAL* 3.6 25.3 - - + +
154A GLN* 3.9 5.9 - - - +
156A TRP* 3.2 22.2 + - - -
392A ARG* 3.7 31.9 - - - +
400A LYS* 5.7 3.4 - - - +
602A PO4 5.1 5.5 + - - -
193B PHE 4.9 5.4 - - - +
195B TYR* 1.3 78.3 - - - +
197B GLY* 1.3 61.5 + - - +
198B VAL 3.5 0.4 - - - -
246B GLU* 5.6 0.2 + - - -
601B LTS 3.4 23.5 + - - -
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Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TRP* 3.2 23.2 - - - -
391A THR* 5.7 0.2 - - - -
392A ARG* 4.1 19.7 + - - +
194B GLY* 3.0 11.9 + - - -
196B ARG* 1.3 81.3 - - - +
198B VAL* 1.3 60.3 + - - +
384B GLY* 4.7 11.7 - - - -
388B GLN* 3.3 17.2 - - - +
606B EDO 6.2 1.6 - - - -
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLN* 3.7 13.2 - - - +
156A TRP* 2.9 18.1 + - - -
157B TYR* 4.3 0.2 - - - +
194B GLY 3.5 8.5 - - - +
195B TYR* 3.4 17.9 - - - +
196B ARG 3.5 0.2 - - - -
197B GLY* 1.3 81.5 - - - +
199B SER* 1.3 62.3 + - - +
200B SER 3.5 21.0 + - - +
203B THR* 3.9 13.7 - - + -
204B ALA* 3.7 17.7 - - + -
387B LEU* 3.4 48.5 - - + +
388B GLN* 3.4 5.2 - - + +
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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