Contacts of the strand formed by residues 324 - 328 (chain C) in PDB entry 3QNF
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 324 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ILE* 3.7 22.9 - - + +
217C SER* 3.6 41.7 - - - +
218C ASN* 4.4 2.7 - - - -
248C ALA* 3.8 24.5 - - + +
249C PHE* 4.2 1.3 - - - +
250C ILE* 3.6 30.7 - - + -
305C LYS* 4.2 0.7 - - - +
307C ASP* 3.3 16.2 - - + +
309C ALA* 4.4 3.1 - - + -
321C ASN* 3.1 25.6 + - - +
322C TRP 3.2 2.0 - - - +
323C GLY* 1.3 80.2 - - - +
325C THR* 1.3 68.2 + - - +
326C THR* 3.9 2.2 - - + +
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Residues in contact with THR 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C GLN* 2.8 24.5 + - - +
307C ASP 2.8 12.1 + - - +
308C LEU* 3.3 4.2 - - - +
309C ALA* 2.8 25.5 + - - +
319C MET 3.5 14.4 - - - +
320C GLU* 4.0 0.7 - - - -
321C ASN 3.8 4.0 - - - +
324C LEU* 1.3 74.4 - - - +
326C THR* 1.3 61.3 + - - +
327C TYR* 2.8 34.7 + - - +
354C GLU* 3.8 11.4 - - + +
355C LEU* 4.7 0.9 - - + -
358C GLN* 3.4 28.5 - - - +
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Residues in contact with THR 326 (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* 5.1 0.7 - - - +
180C THR* 4.8 9.1 + - - +
181C GLN* 4.4 0.9 + - - -
248C ALA* 5.5 1.8 - - + -
250C ILE* 4.1 26.0 - - + -
309C ALA* 3.5 6.7 - - + -
311C ILE* 4.1 14.8 - - + -
314C PHE* 3.6 14.1 - - - -
318C ALA* 3.1 4.5 - - - +
319C MET* 2.8 42.7 + - - +
321C ASN* 3.2 17.5 + - - +
324C LEU* 3.9 10.8 - - + +
325C THR* 1.3 77.5 - - - +
327C TYR* 1.3 61.5 + - - +
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Residues in contact with TYR 327 (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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308C LEU* 3.2 31.8 - - + +
309C ALA 2.6 20.9 + - - +
310C ALA* 3.5 0.3 - - - -
311C ILE* 2.9 29.1 + - - +
314C PHE* 4.1 5.6 - - - -
317C GLY 3.9 5.6 - - - +
318C ALA* 3.4 18.2 - - + +
325C THR* 2.8 42.3 + - - +
326C THR* 1.3 75.9 - - - +
328C ARG* 1.3 69.3 + - - +
331C ALA* 4.5 5.8 - - + -
332C LEU* 3.6 25.8 - - + -
350C THR* 3.7 14.4 - - + -
351C VAL* 4.0 17.5 + - + +
354C GLU* 3.4 29.5 - - + +
355C LEU* 4.7 2.1 - - - +
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Residues in contact with ARG 328 (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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310C ALA* 5.0 0.2 - - - -
311C ILE 3.9 0.9 - - - -
312C PRO 5.5 1.1 - - - +
314C PHE* 3.8 31.4 - - + +
316C SER 4.5 5.2 - - - +
317C GLY* 3.0 24.7 + - - +
327C TYR* 1.3 76.1 - - - +
329C GLU* 1.3 61.9 + - - +
330C SER* 3.5 22.0 - - - +
331C ALA* 2.8 42.4 + - + +
332C LEU* 3.5 3.8 + - - +
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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