Contacts of the strand formed by residues 204 - 213 (chain C) in PDB entry 4LCC
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 THR 204 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C HIS* 3.3 35.8 - - + +
32C PRO* 4.6 7.4 - - + -
33C PRO* 4.2 11.2 - - + -
123C LEU* 4.7 6.5 - - - -
124C GLY 3.6 7.4 - - - -
125C ILE* 3.8 17.7 - - + -
190C LEU* 4.8 1.3 - - - -
203C HIS* 1.3 81.2 - - - +
205C TYR* 1.3 61.6 + - - +
206C GLN* 3.8 4.7 + - - -
227C TYR* 3.5 12.0 - - - -
228C ASP* 3.0 34.9 + - - +
229C GLY 3.7 1.2 + - - -
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Residues in contact with TYR 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG 3.5 0.7 - - - +
123C LEU* 3.5 1.9 - - - -
124C GLY* 2.7 35.5 + - - -
186C PHE* 3.2 51.6 - + + -
189C GLU* 3.1 34.5 + - + +
190C LEU* 3.7 24.5 - - + -
193C LEU* 3.4 31.8 - - + +
203C HIS 4.4 0.2 + - - -
204C THR* 1.3 74.7 - - - +
206C GLN* 1.3 62.3 + - - +
225C TYR* 3.1 35.8 - + + +
226C ALA 3.3 17.0 - - - -
227C TYR* 4.3 2.7 - + - -
232C PHE* 4.9 7.0 - + - -
256C TRP* 4.7 6.2 - - - -
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Residues in contact with GLN 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C HIS* 3.4 21.4 - - - -
55C PHE* 4.7 8.2 - - + +
59C TRP* 2.8 52.7 + - + +
60C SER 4.7 0.2 + - - -
61C PHE* 3.3 23.1 - - - -
121C PHE* 6.0 2.3 - - + -
122C ARG 3.1 7.2 - - - +
123C LEU* 3.5 17.9 - - + -
186C PHE* 4.2 2.5 - - - -
204C THR* 3.8 2.1 + - - +
205C TYR* 1.3 80.8 - - - +
207C ARG* 1.3 60.8 + - - +
225C TYR* 3.2 5.3 - - - +
226C ALA* 2.6 43.3 + - + +
229C GLY* 3.7 14.6 + - - -
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Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C TRP* 4.0 1.6 - - - -
120C TYR 3.5 1.6 + - - +
121C PHE* 3.3 9.4 - - - -
122C ARG* 2.9 63.6 + - + +
186C PHE* 3.7 16.0 - - + -
206C GLN* 1.3 74.3 - - - +
208C MET* 1.3 63.1 - - - +
209C ILE* 3.5 26.1 - - - +
223C LEU* 3.5 28.4 - - + +
224C GLN 3.4 6.5 - - - +
225C TYR* 2.8 42.6 + - + -
266C GLN* 4.5 5.1 + - - +
401C 1XL 3.2 50.2 + - - -
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Residues in contact with MET 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LYS* 4.3 20.4 - - + +
59C TRP* 3.6 17.9 - - + -
119C ARG* 4.2 9.0 - - + +
120C TYR 3.4 4.7 - - - +
121C PHE* 3.7 32.8 - - + -
207C ARG* 1.3 75.8 - - - +
209C ILE* 1.3 62.7 + - - +
222C PHE* 3.9 32.7 - - + +
223C LEU* 3.2 5.8 - - - +
224C GLN* 2.7 78.8 + - + +
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Residues in contact with ILE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ARG* 3.6 2.3 - - - +
120C TYR* 2.8 50.0 + - + +
207C ARG* 3.5 28.3 - - - +
208C MET* 1.3 74.6 - - - +
210C GLY* 1.3 61.6 + - - +
222C PHE* 3.3 13.4 - - - +
223C LEU* 3.7 12.6 - - + -
266C GLN* 4.6 4.5 - - - +
269C TRP* 3.5 22.9 - - + -
270C LEU* 3.5 20.6 - - + -
401C 1XL 2.9 34.3 - - + +
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Residues in contact with GLY 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 3.1 14.8 - - - -
120C TYR* 5.6 0.4 - - - -
209C ILE* 1.3 81.7 - - - +
211C CYS* 1.3 60.9 + - - +
221C GLY* 3.4 1.9 - - - -
222C PHE* 2.9 43.7 + - - +
269C TRP* 4.7 3.1 - - - -
270C LEU* 4.2 4.2 - - - +
274C CYS* 3.9 9.4 - - - -
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Residues in contact with CYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C SER* 3.6 0.3 - - - -
118C LEU* 2.8 33.1 + - - +
210C GLY* 1.3 74.5 - - - +
212C GLU* 1.3 61.9 + - - +
220C THR 3.3 15.3 - - - +
221C GLY* 4.4 0.9 - - - -
222C PHE* 3.9 4.3 - - - -
270C LEU 3.8 7.0 - - - +
274C CYS* 2.0 60.3 - - + -
275C ILE* 3.4 21.5 - - + -
278C LEU* 4.0 4.8 - - - +
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Residues in contact with GLU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C THR* 4.0 14.6 + - - +
116C HIS 3.5 6.3 - - - +
117C SER* 3.3 25.9 - - - +
119C ARG* 4.3 16.4 + - - -
211C CYS* 1.3 73.0 - - - +
213C LEU* 1.3 60.2 + - - +
214C LEU* 4.0 13.4 + - + +
219C ILE* 3.4 6.8 - - - +
220C THR* 3.1 50.5 + - - +
222C PHE* 4.6 10.7 - - + -
275C ILE* 4.9 2.0 - - - -
278C LEU* 4.4 1.8 - - - -
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C THR* 3.4 1.2 - - - -
116C HIS* 2.8 41.5 + - + +
212C GLU* 1.3 71.2 - - - +
214C LEU* 1.3 90.5 + - - +
217C GLY* 3.5 28.0 - - - +
218C SER 3.6 2.0 - - - +
219C ILE* 3.8 13.2 - - + -
275C ILE* 4.4 6.3 - - + -
278C LEU* 4.1 14.2 - - + +
279C LYS* 3.6 38.4 - - + -
282C LEU* 5.9 4.5 - - + -
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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