Contacts of the strand formed by residues 335 - 339 (chain C) in PDB entry 2INU
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 HIS 335 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304B ARG* 3.3 38.9 - - + +
305B CYS 3.8 11.8 + - - -
306B SER* 4.3 15.9 + - - -
328B GLU 2.8 30.3 + - - -
330B LEU* 4.1 5.2 - - + +
310C ASN 2.9 12.8 + - - +
311C ARG* 4.5 11.4 - - + -
312C LEU* 2.7 36.9 + - - +
334C ASN* 1.3 71.6 - - - +
336C ILE* 1.3 67.8 + - - +
337C ARG* 4.2 8.0 - - + +
373C LEU* 3.8 26.2 + - + +
375C ALA* 4.1 9.7 - - + +
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Residues in contact with ILE 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LEU* 3.7 14.8 - - + -
319C MSE 3.7 12.1 - - + -
320C LEU* 5.2 7.4 - - + -
331C ILE* 5.5 2.2 - - + -
334C ASN* 4.2 14.6 - - + +
335C HIS* 1.3 77.2 - - - +
337C ARG* 1.3 62.1 + - - +
338C ARG 4.2 0.3 + - - -
359C VAL* 3.5 32.5 - - + -
360C VAL* 4.2 11.2 - - + -
369C ILE* 6.2 0.4 - - + -
372C ASN* 4.0 20.4 - - + +
373C LEU 2.9 10.5 + - - +
374C PHE* 3.2 40.7 - - + +
375C ALA 2.8 24.4 + - - +
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Residues in contact with ARG 337 (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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280B GLU* 4.0 10.8 + - - -
304B ARG* 3.6 44.3 - - + +
328B GLU* 4.7 1.6 + - - -
311C ARG* 6.0 2.2 - - - +
312C LEU 2.9 15.2 + - - +
313C GLN* 3.3 18.1 + - + -
314C GLY 3.0 25.8 + - - +
319C MSE 3.3 4.5 - - - +
335C HIS* 4.2 9.9 - - + -
336C ILE* 1.3 75.0 - - - +
338C ARG* 1.3 65.5 + - - +
339C THR* 3.4 24.2 + - - +
375C ALA* 2.9 43.2 + - + +
376C TYR 3.9 0.4 - - - +
377C ASN* 3.1 35.1 + - - +
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Residues in contact with ARG 338 (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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314C GLY 3.6 3.6 - - - -
315C PHE 3.1 22.9 + - - -
316C TYR* 3.6 24.5 - - - +
317C PRO* 3.5 21.2 - - - +
319C MSE 3.8 10.5 - - - -
336C ILE 4.2 1.0 + - - -
337C ARG* 1.3 75.3 + - - +
339C THR* 1.3 82.6 + - - +
340C ASN* 4.9 2.4 - - - +
355C ASP* 3.1 28.3 + - - -
359C VAL* 4.2 14.5 - - + +
375C ALA 3.0 8.3 + - - +
376C TYR* 3.5 30.6 - - + -
377C ASN 3.0 24.8 + - - -
378C VAL* 3.8 21.3 - - + +
382C ASN* 5.4 4.0 + - - +
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Residues in contact with THR 339 (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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313C GLN* 4.7 10.3 - - + +
314C GLY 3.1 5.4 + - - +
315C PHE* 3.1 39.8 - - + +
337C ARG* 3.4 29.0 + - + +
338C ARG* 1.3 96.5 + - - +
340C ASN* 1.3 74.2 + - - +
377C ASN* 3.0 20.0 + - - +
378C VAL* 3.8 4.3 - - - -
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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