Contacts of the strand formed by residues 276 - 280 (chain C) in PDB entry 3QN3
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 ILE 276 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C ILE* 4.1 9.9 - - + -
236C ILE* 3.2 23.3 - - + +
238C LEU* 3.9 23.1 - - + -
270C LEU* 3.9 36.8 - - + +
271C CYS* 4.0 15.5 - - - +
274C TYR* 2.8 23.5 + - + +
275C PRO* 1.3 70.9 - - - +
277C CYS* 1.3 60.5 + - - +
278C SER 3.7 10.1 - - - +
279C ILE* 3.7 30.5 - - + -
302C ILE* 3.8 16.2 - - + +
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Residues in contact with CYS 277 (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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167C MET* 3.6 31.4 - - - -
169C PHE* 3.9 17.3 - - + -
235C LYS* 4.2 23.6 - - + -
236C ILE 2.9 17.4 + - - -
275C PRO 3.6 1.2 + - - -
276C ILE* 1.3 72.9 - - - +
278C SER* 1.3 63.6 + - - +
301C LYS 5.8 0.2 - - - -
302C ILE* 3.7 7.7 - - - +
303C GLN* 2.9 28.6 + - - +
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Residues in contact with SER 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C MET* 4.1 6.3 - - - +
167C MET* 4.8 0.2 - - - -
236C ILE 3.9 0.4 + - - -
237C ALA* 3.5 20.4 - - - -
238C LEU 2.9 24.7 + - - -
276C ILE* 3.6 4.8 - - - +
277C CYS* 1.3 88.2 - - - +
279C ILE* 1.3 70.1 + - - +
280C GLU 5.0 0.2 + - - -
302C ILE* 4.6 0.4 - - - +
303C GLN* 2.9 36.0 + - - +
305C VAL* 3.3 13.9 - - - +
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Residues in contact with ILE 279 (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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238C LEU* 3.5 13.0 - - + +
240C VAL* 3.9 26.2 - - + -
267C TYR* 3.9 36.8 - - + -
270C LEU* 6.1 0.9 - - + -
271C CYS* 3.9 11.7 - - - -
276C ILE* 3.7 11.4 - - + -
278C SER* 1.3 82.9 + - - +
280C GLU* 1.3 62.5 + - - +
281C ASP 4.1 0.2 + - - -
282C GLY* 4.2 17.1 + - - -
291C TRP* 5.4 1.0 - - - -
294C LEU* 6.3 0.2 - - + -
302C ILE* 3.5 25.1 - - + -
303C GLN 2.9 7.5 + - - -
304C LEU* 3.4 14.4 - - + +
305C VAL 2.9 21.7 + - - +
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Residues in contact with GLU 280 (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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145C MET* 5.2 2.8 - - - +
165C MET* 4.7 3.3 - - + +
238C LEU 2.8 17.6 + - - +
239C ASP* 2.8 32.2 - - - +
240C VAL* 3.1 24.4 + - - +
278C SER* 4.2 0.4 - - - +
279C ILE* 1.3 71.3 - - - +
281C ASP* 1.3 69.7 + - - +
282C GLY* 3.1 3.9 + - - -
305C VAL* 3.3 24.9 - - + +
307C ASP* 2.9 37.5 - - + +
330C LEU* 3.4 10.4 - - - +
383C LYS* 2.8 30.1 + - - +
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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