Contacts of the strand formed by residues 360 - 364 (chain C) in PDB entry 3MA2
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 PHE 360 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328C GLU* 5.2 5.6 - - - -
337C ARG* 3.3 58.8 - - - -
338C TYR 3.1 7.4 - - - +
339C GLU* 3.6 41.5 - - + -
340C ILE* 3.9 3.1 - - - +
358C ILE* 3.6 17.2 - - - +
359C ARG* 1.3 111.9 - - + +
361C VAL* 1.3 60.3 - - - +
362C TYR* 3.9 17.2 - - + -
394C LEU* 4.1 8.3 + - - +
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Residues in contact with VAL 361 (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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323C PHE* 4.3 9.2 - - + -
336C GLN 4.1 0.2 - - - +
337C ARG* 3.3 4.0 - - - -
338C TYR* 2.9 57.8 + - + +
340C ILE* 4.2 16.5 - - + +
360C PHE* 1.3 75.6 - - - +
362C TYR* 1.3 61.2 + - - +
385C ILE* 4.6 4.7 - - + -
394C LEU* 3.4 37.9 - - + +
396C ILE* 3.7 34.5 - - + -
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Residues in contact with TYR 362 (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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335C TYR* 4.7 9.4 - + + -
336C GLN 3.6 5.6 - - - +
337C ARG* 3.2 50.0 + - + -
360C PHE* 3.9 20.7 - - + +
361C VAL* 1.3 75.4 - - - +
363C THR* 1.3 61.3 + - - +
393C LEU* 3.9 45.3 - - + +
394C LEU 2.7 18.9 + - - +
395C HIS* 3.2 31.4 + + + -
396C ILE* 2.9 29.1 + - - +
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Residues in contact with THR 363 (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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335C TYR* 3.3 10.5 - - - -
336C GLN* 2.6 61.6 + - + +
338C TYR* 3.9 13.2 - - + -
362C TYR* 1.3 76.6 - - - +
364C PRO* 1.4 69.8 - - - +
371C GLY* 3.7 0.2 - - - -
372C TYR* 3.0 38.6 + - + +
396C ILE* 2.6 27.8 + - + -
397C THR* 3.9 0.5 - - - -
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Residues in contact with PRO 364 (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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334C LEU 3.5 10.8 - - - +
335C TYR* 3.8 12.3 - - + +
336C GLN* 3.1 10.9 + - - -
363C THR* 1.4 97.0 - - - +
365C ALA* 1.3 61.5 + - - +
366C MET 3.3 4.0 - - - +
369C VAL* 3.6 30.5 - - + +
370C CYS* 3.9 11.0 - - + +
371C GLY* 3.1 22.3 - - - +
395C HIS* 5.9 0.4 - - - +
396C ILE 4.0 4.7 - - - +
397C THR* 5.0 5.4 - - + -
190D THR* 3.7 26.0 - - + +
198D PHE* 6.3 1.1 - - + -
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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