Contacts of the helix formed by residues 195 - 202 (chain D) in PDB entry 4LQL
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 LYS 195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B ASP* 3.9 11.4 + - - +
192B GLU* 5.0 17.0 - - + +
193B GLY 5.4 0.8 + - - -
195B LYS* 4.2 19.1 - - - +
87C LYS* 5.1 15.2 - - - +
180D ARG* 2.9 36.4 - - - +
183D ASP* 4.4 0.2 + - - -
184D THR* 5.1 2.0 + - - -
192D GLU* 5.7 4.4 - - - +
193D GLY 3.9 8.0 + - - +
194D ASP* 1.3 79.4 + - - +
196D VAL* 1.3 67.9 + - + +
197D ALA 3.3 1.6 - - - -
198D ALA* 3.5 7.1 + - - +
199D GLN* 3.3 25.3 + - - +
204D TRP 4.9 0.5 - - - +
206D VAL* 3.7 40.8 - - + +
309D PHE* 4.6 9.6 - - + -
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Residues in contact with VAL 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ALA* 3.7 31.6 - - + +
192B GLU* 3.6 35.2 - - + +
87C LYS* 5.5 7.4 - - + +
90C ILE* 3.7 9.1 - - + +
135C TYR* 5.7 1.8 - - + -
136C ILE* 4.0 17.3 - - + -
139C ARG* 4.0 18.2 - - + +
194D ASP* 3.3 17.5 - - - +
195D LYS* 1.3 80.0 - - + +
197D ALA* 1.3 56.3 + - - +
199D GLN* 5.0 0.2 - - - -
200D ILE* 3.1 32.3 + - + +
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B ASP* 5.6 4.7 - - + -
139C ARG* 3.6 12.1 - - - +
194D ASP* 2.9 27.3 + - + +
195D LYS 3.3 0.2 - - - -
196D VAL* 1.3 74.6 - - - +
198D ALA* 1.3 56.0 + - - +
199D GLN 3.0 2.0 - - - -
200D ILE* 4.1 7.0 - - + +
201D LYS* 2.6 44.4 + - + +
399D GLY* 5.6 8.3 - - - -
400D TYR* 4.0 9.2 - - + +
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Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ASP 4.0 3.8 - - - +
195D LYS* 3.5 10.4 + - - +
197D ALA* 1.3 75.0 - - - +
199D GLN* 1.3 54.3 + - - +
202D LEU* 2.8 38.3 + - + +
204D TRP* 3.5 19.2 + - + +
206D VAL* 6.1 3.8 - - + -
310D LYS* 6.5 0.9 - - + -
400D TYR* 3.0 36.4 + - + +
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Residues in contact with GLN 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ALA* 5.4 6.8 - - - +
87C LYS* 3.2 49.7 - - - +
88C ASN* 5.1 0.3 - - - -
90C ILE* 3.3 32.3 - - + +
91C ARG* 4.9 3.8 + - + +
94C GLU* 5.4 0.2 - - - +
195D LYS 3.3 15.4 + - - +
196D VAL* 5.0 0.4 - - - +
197D ALA 3.0 0.6 - - - -
198D ALA* 1.3 74.3 - - - +
200D ILE* 1.3 67.5 + - - +
201D LYS 3.2 0.9 - - - -
203D GLY* 3.3 24.3 - - - +
204D TRP 2.8 25.5 + - - +
205D THR* 3.6 23.5 + - - +
206D VAL 4.8 1.2 - - - +
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Residues in contact with ILE 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ILE* 3.8 18.8 - - + -
94C GLU* 4.1 18.6 - - + +
136C ILE* 4.7 3.6 - - + -
139C ARG* 3.6 42.8 - - + +
140C LEU* 4.3 21.8 - - + -
196D VAL 3.1 22.5 + - - +
197D ALA* 3.0 10.0 + - + +
199D GLN* 1.3 78.1 - - - +
201D LYS* 1.3 73.5 + - + +
203D GLY* 4.3 1.9 + - - -
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Residues in contact with LYS 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ALA* 2.6 28.2 + - + +
198D ALA* 4.5 1.8 - - - -
200D ILE* 1.3 84.4 - - + +
202D LEU* 1.3 60.4 + - + +
203D GLY 3.4 2.7 + - - -
399D GLY* 6.1 4.9 - - - -
400D TYR* 4.7 13.5 - - + +
466D PHE* 3.4 41.4 + - - +
467D LYS* 3.2 30.5 + - - +
468D VAL* 4.1 18.6 - - + -
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Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D SER* 4.0 19.6 - - - -
174D PHE* 4.2 3.3 + - - -
198D ALA* 2.8 20.6 + - + +
201D LYS* 1.3 80.8 - - + +
203D GLY* 1.3 51.2 + - - +
204D TRP* 2.7 30.8 + - + +
393D LEU* 4.5 22.0 - - + -
400D TYR* 5.3 4.5 - - + -
466D PHE* 4.7 22.4 - - + -
468D VAL* 5.0 8.1 - - + -
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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