Contacts of the strand formed by residues 316 - 322 (chain C) in PDB entry 3KQG
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 LEU 316 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C SER* 3.3 13.2 - - - +
211C LEU* 3.5 34.8 - - - +
212C ILE 3.6 12.1 - - - -
213C PRO* 3.8 8.9 - - + +
249C LEU* 4.0 32.8 - - + -
250C ILE 3.7 8.4 + - - +
251C TYR* 3.0 31.0 - - + +
252C TRP* 2.7 28.9 + - - -
315C PHE* 1.3 78.7 - - - +
317C PHE* 1.3 53.4 + - - +
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Residues in contact with PHE 317 (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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208C TYR* 3.4 3.3 - + - +
210C SER* 2.9 49.1 + - - -
212C ILE* 3.5 23.6 - - + -
214C LYS* 3.6 23.6 - - + -
219C ALA* 3.5 27.6 - - + -
222C PHE* 3.3 46.7 - + + -
223C CYS* 3.9 16.8 - - - -
230C LEU* 3.9 3.8 - - + -
251C TYR* 3.6 3.6 - - - -
252C TRP* 3.6 17.5 - - + +
315C PHE 4.0 6.1 - - - +
316C LEU* 1.3 77.8 - - - +
318C ILE* 1.3 64.1 + - - +
319C CYS* 3.7 10.1 - - - -
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Residues in contact with ILE 318 (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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207C TYR* 4.2 11.0 - - + -
208C TYR 3.1 5.8 - - - +
209C PHE* 3.3 37.9 - - + -
223C CYS* 4.4 0.7 - - - -
230C LEU* 3.3 8.7 - - - +
231C THR* 2.9 43.6 + - + +
242C LEU* 4.3 14.1 - - + +
246C ALA* 5.0 0.7 - - + -
251C TYR* 3.5 32.8 - - + -
252C TRP 3.2 8.5 + - - +
253C ILE* 4.6 2.7 - - + -
298C ILE* 4.5 14.8 - - + -
317C PHE* 1.3 77.9 - - - +
319C CYS* 1.3 73.9 + - - +
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Residues in contact with CYS 319 (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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199C TRP* 4.3 4.7 - - + -
206C PHE 4.4 0.2 - - - -
207C TYR* 3.1 5.9 - - - -
208C TYR* 2.8 47.1 + - + -
222C PHE* 4.2 4.9 - - - -
223C CYS* 2.0 49.4 - - - -
226C ARG* 5.6 1.1 - - - -
228C SER* 3.1 17.9 - - - +
229C HIS 3.2 4.9 - - - -
317C PHE* 3.7 17.3 - - - -
318C ILE* 1.3 78.5 - - - +
320C LYS* 1.3 60.5 + - - +
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Residues in contact with LYS 320 (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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199C TRP* 5.0 0.2 - - - -
205C ASN* 3.7 33.3 - - + +
206C PHE 3.2 8.1 - - - +
207C TYR* 3.7 11.0 - - + -
228C SER* 3.0 15.6 - - - -
229C HIS* 2.7 20.5 + - + +
230C LEU 5.0 0.2 - - - +
231C THR* 3.4 27.6 - - - +
232C SER* 3.1 31.0 + - - +
234C THR* 4.1 6.9 + - - +
238C GLU* 2.5 35.8 + - - -
268C ASP* 4.5 5.8 - - - +
319C CYS* 1.3 76.8 - - - +
321C ARG* 1.3 63.1 + - - +
322C PRO* 5.9 0.2 - - + -
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Residues in contact with ARG 321 (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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194C VAL* 4.0 20.4 - - - +
199C TRP* 3.5 23.7 - - + -
205C ASN* 3.6 5.4 - - - -
206C PHE* 2.7 78.0 + - + +
226C ARG 3.8 13.5 + - - -
227C ASN* 3.3 41.5 - - - +
228C SER* 3.5 4.7 - - - -
320C LYS* 1.3 77.4 - - - +
322C PRO* 1.3 75.4 + - + +
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Residues in contact with PRO 322 (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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204C GLY 3.8 2.0 - - - +
205C ASN* 3.3 18.4 - - - +
206C PHE* 4.3 5.2 - - - -
320C LYS* 5.9 0.4 - - + -
321C ARG* 1.3 94.3 + - + +
323C TYR* 1.3 66.8 + - - +
324C VAL* 3.4 16.8 + - + +
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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