Contacts of the strand formed by residues 335 - 347 (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 TYR 335 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329C VAL* 4.1 0.3 - - - -
330C ASN* 2.9 30.2 + - + +
333C THR* 3.2 25.1 + - - +
334C LEU* 1.3 77.1 - - - +
336C GLN* 1.3 61.6 + - - +
362C TYR* 4.7 9.6 - + + -
363C THR 3.3 26.7 - - - -
364C PRO* 3.7 18.1 - - + +
365C ALA* 4.0 4.3 - - - +
390C GLN* 4.5 9.7 + - - -
395C HIS* 3.7 31.1 + + - -
189D SER 3.3 21.5 + - - -
190D THR* 3.1 28.9 + - + -
191D PRO* 4.1 8.4 - - + +
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Residues in contact with GLN 336 (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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327C PRO* 3.4 24.7 - - + +
328C GLU 3.4 12.8 - - - +
329C VAL* 4.0 18.6 - - + +
335C TYR* 1.3 74.7 - - - +
337C ARG* 1.3 63.7 + - - +
338C TYR* 4.0 7.7 + - + -
362C TYR* 3.6 3.8 - - - +
363C THR* 2.6 51.8 + - + +
364C PRO 3.1 18.5 + - - +
365C ALA* 3.8 7.6 - - - +
372C TYR 3.5 16.4 + - - -
373C PHE* 3.5 33.3 - - - -
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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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326C THR 4.5 0.3 - - - +
327C PRO* 3.3 3.4 - - - +
328C GLU* 2.9 66.0 + - + +
336C GLN* 1.3 75.7 - - - +
338C TYR* 1.3 64.0 + - - +
360C PHE* 3.3 49.5 - - - -
361C VAL 3.3 11.4 - - - +
362C TYR* 3.2 44.7 + - + -
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Residues in contact with TYR 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C PHE* 3.8 26.5 - + + -
325C GLY 4.3 7.0 - - - -
327C PRO* 3.7 43.4 - - + +
336C GLN* 4.0 7.9 + - - -
337C ARG* 1.3 75.8 - - - +
339C GLU* 1.3 62.9 + - - +
340C ILE 3.7 0.3 + - - -
360C PHE* 3.1 7.8 - - - +
361C VAL* 2.9 54.0 + - + +
363C THR* 3.9 17.0 - - + -
372C TYR* 2.7 37.0 + + - -
373C PHE* 3.2 4.3 - - - -
374C HIS* 3.1 37.8 + - + -
396C ILE* 5.5 0.2 - - + -
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Residues in contact with GLU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C PHE* 4.0 1.2 - - - -
324C VAL* 3.1 44.5 + - + +
325C GLY* 4.0 10.1 + - - +
326C THR 5.4 2.4 + - - -
328C GLU* 5.5 4.2 - - - +
337C ARG 4.2 0.8 + - - -
338C TYR* 1.3 75.3 - - - +
340C ILE* 1.3 69.3 + - - +
359C ARG* 3.4 23.9 + - + +
360C PHE* 3.6 28.7 - - + -
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Residues in contact with ILE 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ILE* 3.7 28.9 - - + -
321C ALA* 4.0 11.0 - - + -
322C LYS 3.2 14.1 - - - +
323C PHE* 3.9 27.1 - - + -
324C VAL* 4.4 6.0 - - - +
338C TYR 4.1 6.5 - - - +
339C GLU* 1.3 84.7 - - - +
341C LYS* 1.4 58.5 + - - +
342C MET 5.0 0.7 - - - +
358C ILE* 3.6 28.9 - - + +
359C ARG* 3.0 33.3 + - - +
360C PHE* 3.9 5.6 - - - +
361C VAL* 4.2 10.1 - - + -
385C ILE* 4.4 10.5 - - + -
394C LEU* 4.8 0.2 - - + -
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Residues in contact with LYS 341 (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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321C ALA* 3.3 2.0 - - - -
322C LYS* 3.0 45.2 + - + +
324C VAL* 4.0 19.0 - - + +
340C ILE* 1.4 71.5 - - - +
342C MET* 1.3 75.5 + - - +
343C THR* 3.5 8.6 + - + +
357C ASP* 4.8 13.4 + - - +
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Residues in contact with MET 342 (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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319C ILE* 3.9 29.6 - - + -
320C ARG 3.6 13.0 - - - +
321C ALA* 4.0 4.5 - - - +
340C ILE 4.0 1.8 - - - -
341C LYS* 1.3 89.6 + - - +
343C THR* 1.3 61.0 + - - +
344C LYS* 4.0 10.3 - - - +
345C MET* 4.1 23.3 - - + +
355C ALA* 4.8 6.5 - - + +
356C ALA 3.5 22.0 - - - +
357C ASP* 3.8 19.8 + - + +
358C ILE* 3.7 33.1 + - - +
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Residues in contact with THR 343 (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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320C ARG* 2.9 17.3 + - - +
321C ALA* 4.0 0.6 + - - -
322C LYS* 4.3 17.7 - - + +
341C LYS* 4.0 15.3 - - + +
342C MET* 1.3 78.0 - - - +
344C LYS* 1.3 68.5 + - - +
382C GLU* 2.9 40.0 + - - +
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Residues in contact with LYS 344 (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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319C ILE* 3.3 6.4 - - - +
320C ARG* 2.9 41.5 + - + +
342C MET* 3.7 8.6 - - - -
343C THR* 1.3 85.6 + - - +
345C MET* 1.3 72.1 + - - +
346C TYR* 3.6 37.5 + - + +
349C PHE* 6.1 1.1 - - - -
417C THR* 6.3 1.3 - - - -
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Residues in contact with MET 345 (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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317C LEU* 3.6 24.9 - - + -
318C VAL 4.0 3.8 - - - +
319C ILE* 4.1 4.7 - - + -
342C MET* 4.1 20.9 - - + +
344C LYS* 1.3 85.0 - - - +
346C TYR* 1.4 64.1 + - - +
347C LYS 3.4 19.1 - - - +
348C GLY 3.5 30.7 - - - +
349C PHE* 3.2 37.8 - - + -
355C ALA* 4.2 11.0 - - + -
356C ALA* 3.6 30.1 - - + +
358C ILE* 4.4 2.9 - - + -
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Residues in contact with TYR 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C PHE* 3.8 12.1 - - + -
318C VAL* 2.8 25.5 + - + +
319C ILE 4.7 2.7 - - - -
320C ARG* 3.1 43.0 + - + -
344C LYS* 3.6 29.0 - - + +
345C MET* 1.4 76.5 - - - +
347C LYS* 1.3 58.9 + - - +
349C PHE* 3.8 13.4 - - - -
384C LEU* 3.9 21.1 - - + -
405C TRP* 3.3 33.5 - + - -
416C PHE* 3.4 26.2 - - + +
417C THR* 4.0 25.5 + - + +
421C THR* 4.6 5.9 - - - +
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Residues in contact with LYS 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C PHE* 2.8 53.5 + - + +
313C CYS* 2.9 21.6 + - - +
315C SER 2.9 21.4 + - - +
316C ASP* 3.9 10.3 - - - +
317C LEU* 3.4 4.0 - - - +
318C VAL* 3.0 34.6 + - + +
345C MET* 3.4 14.4 - - - +
346C TYR* 1.3 77.4 - - - +
348C GLY* 1.3 62.1 + - - +
349C PHE* 3.8 8.1 - - - -
424C CYS* 5.0 2.6 - - - +
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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