Contacts of the strand formed by residues 194 - 203 (chain C) in PDB entry 4LL4
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 GLU 194 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186C ARG* 4.7 2.6 + - - -
189C PHE* 4.2 10.6 - - - -
192C GLY 3.8 0.8 + - - -
193C ASP* 1.3 79.9 - - - +
195C ILE* 1.3 65.7 + - - +
196C SER* 3.7 8.0 + - - +
254C SER* 3.2 33.5 + - - +
255C LEU 3.4 16.2 - - - +
256C ARG* 2.5 36.5 + - - +
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Residues in contact with ILE 195 (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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184C ILE* 3.7 29.6 - - + -
189C PHE* 3.8 42.0 - - + -
194C GLU* 1.3 74.2 - - - +
196C SER* 1.3 58.9 + - - +
197C ILE* 3.6 4.1 + - + +
215C ILE* 4.1 26.7 - - + -
253C LYS 3.4 2.6 - - - +
254C SER* 3.2 3.4 - - - -
255C LEU* 2.6 49.6 + - + +
257C VAL* 4.0 9.0 - - + -
276C LEU* 4.0 15.5 - - + -
294C LEU* 4.2 17.5 - - + -
296C ILE* 5.7 0.2 - - + -
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Residues in contact with SER 196 (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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183C ARG 4.1 1.2 - - - +
184C ILE* 4.0 15.6 - - - +
185C ASP* 4.9 13.1 + - - +
189C PHE* 5.4 0.8 - - - -
194C GLU* 3.7 9.5 + - - +
195C ILE* 1.3 71.4 - - - +
197C ILE* 1.3 61.3 + - - +
198C HIS* 3.8 14.0 + - - -
252C GLY* 3.7 19.9 + - - -
253C LYS 3.5 4.5 - - - -
254C SER* 4.2 6.8 - - - +
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Residues in contact with ILE 197 (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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182C ALA* 4.4 0.4 - - + -
183C ARG 4.0 6.3 - - - +
184C ILE* 4.4 2.0 - - + -
195C ILE* 4.1 10.8 - - + +
196C SER* 1.3 72.9 - - - +
198C HIS* 1.3 70.7 + - - +
199C ALA* 4.3 4.0 - - + -
213C ALA* 3.8 26.9 - - + -
237C VAL* 5.3 2.2 - - + -
250C TRP* 3.6 28.4 - - + +
252C GLY* 3.0 5.8 + - - -
253C LYS 2.5 49.5 + - - +
255C LEU* 4.3 11.9 - - + -
276C LEU* 3.7 29.8 - - + -
278C ILE* 3.9 22.0 - - + -
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Residues in contact with HIS 198 (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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182C ALA* 3.2 2.4 - - - +
183C ARG* 2.8 59.3 + - + +
184C ILE* 6.0 0.4 - - - -
196C SER* 4.1 14.7 + - - -
197C ILE* 1.3 70.2 - - - +
199C ALA* 1.3 59.7 + - - +
250C TRP 3.3 5.2 - - - +
251C ARG* 3.9 14.1 - - + +
252C GLY* 3.6 27.0 + - - -
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Residues in contact with ALA 199 (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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180C VAL* 5.1 0.2 - - + -
181C SER 3.2 10.8 - - - +
182C ALA* 4.0 11.4 - - + -
197C ILE* 4.3 3.1 - - + -
198C HIS* 1.3 74.6 - - - +
200C ASP* 1.3 70.9 + - - +
201C PHE* 3.6 29.7 - - + -
249C SER* 3.0 1.4 - - - -
250C TRP* 2.6 50.0 + - + +
278C ILE* 4.9 1.8 - - + -
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Residues in contact with ASP 200 (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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179C SER* 4.7 1.2 + - - -
180C VAL* 3.4 2.4 - - - -
181C SER* 2.8 41.5 + - - +
199C ALA* 1.3 81.5 + - - +
201C PHE* 1.3 62.1 + - - +
202C GLU 4.5 0.2 + - - -
248C ALA 3.6 2.7 - - - -
249C SER* 2.8 21.1 + - - -
250C TRP 5.0 0.7 - - - +
251C ARG* 5.8 0.2 + - - -
31D TRP* 3.6 39.1 + - + -
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Residues in contact with PHE 201 (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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179C SER 3.5 6.5 - - - +
180C VAL* 3.6 29.4 - - + -
199C ALA* 3.6 29.2 - - + -
200C ASP* 1.3 75.0 - - - +
202C GLU* 1.3 60.4 + - - +
211C PRO* 3.4 23.3 - - + -
242C ILE* 3.5 26.8 - - + +
246C THR 4.9 0.2 - - - -
247C CYS* 3.1 7.0 - - - +
248C ALA* 2.9 45.4 + - + +
250C TRP* 3.8 39.9 - + - -
278C ILE* 4.5 7.9 - - + -
279C TYR 4.9 0.9 - - - -
280C VAL* 3.7 19.3 - - + -
31D TRP* 4.7 1.3 - - - -
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Residues in contact with GLU 202 (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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165C GLU* 5.3 6.5 - - - +
177C ARG 4.0 1.5 - - - +
178C VAL* 3.5 5.5 - - - +
179C SER* 3.1 46.4 + - - +
200C ASP 4.4 0.2 - - - -
201C PHE* 1.3 73.3 - - - +
203C ASN* 1.3 64.2 + - - +
204C THR* 4.1 14.6 - - + +
246C THR 3.8 3.6 - - - -
247C CYS* 3.8 14.7 - - - -
31D TRP* 3.7 16.8 - - + +
33D GLY* 3.4 34.6 + - - -
34D PRO* 4.0 6.2 - - + +
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Residues in contact with ASN 203 (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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177C ARG 3.7 3.0 - - - +
178C VAL* 4.1 3.0 - - + +
202C GLU* 1.3 77.0 - - - +
204C THR* 1.3 59.2 + - - +
205C SER* 2.7 43.0 + - - +
207C ARG 2.8 24.4 + - - -
209C VAL* 3.3 36.0 - - + +
242C ILE* 3.3 17.9 + - + -
243C ILE 4.5 0.4 - - - +
244C SER* 3.9 7.8 - - - +
245C GLY* 2.9 22.2 + - - -
246C THR 2.9 22.2 + - - +
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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