Contacts of the strand formed by residues 363 - 368 (chain C) in PDB entry 4P0S
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 ARG 363 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329C ASP* 2.9 41.0 + - + +
330C HIS* 3.3 30.0 + - + +
331C ILE* 3.2 24.8 + - - -
362C GLU* 1.3 73.4 - - - +
364C ARG* 1.3 64.4 + - - +
365C VAL* 4.2 1.6 - - - +
447C PRO 4.5 6.9 - - - -
448C ASN* 2.9 50.5 + - - +
416D GLN* 3.2 19.0 + - - +
417D LEU* 3.2 12.5 + - - +
419D THR 3.7 9.8 + - - -
420D GLU* 4.1 26.3 + - - -
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Residues in contact with ARG 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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331C ILE* 3.9 12.1 - - + -
356C LEU* 3.4 25.6 - - + +
357C LYS* 3.4 46.7 + - - +
361C LEU 3.7 7.9 + - - -
362C GLU* 3.1 46.5 + - - +
363C ARG* 1.3 74.2 - - - +
365C VAL* 1.3 65.3 + - - +
395C ASP 4.1 10.9 + - - -
396C GLY* 4.9 2.7 + - - +
397C PHE* 3.4 43.5 - - + -
398C PHE* 3.0 21.7 + - - +
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Residues in contact with VAL 365 (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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330C HIS* 4.4 11.0 - - + -
331C ILE 2.9 16.8 + - - +
332C VAL* 3.1 46.0 - - + -
333C GLU* 3.1 4.2 + - - +
363C ARG 4.2 5.8 - - - +
364C ARG* 1.3 77.2 - - - +
366C TYR* 1.3 68.9 + - - +
367C LEU* 4.4 0.9 - - - +
397C PHE* 5.0 1.3 - - - -
398C PHE* 3.3 15.3 - - + +
400C LYS 5.6 1.6 - - - +
411C TYR* 4.5 22.4 - - + +
415C LEU* 5.0 2.9 - - + -
416D GLN* 3.3 27.6 - - - +
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Residues in contact with TYR 366 (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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333C GLU* 3.5 39.3 - - + -
335C LYS* 4.3 20.0 - - + +
340C LEU* 5.4 1.6 - - + -
349C PHE* 3.6 31.0 + + - -
352C GLN* 2.9 28.6 + - - +
353C LYS* 3.7 22.0 - - + -
356C LEU* 4.2 6.7 - - + -
365C VAL* 1.3 74.2 - - - +
367C LEU* 1.3 61.3 + - - +
368C VAL* 3.8 13.6 + - + +
391C THR* 4.8 7.0 - - + -
397C PHE* 3.4 33.2 - + + -
398C PHE 2.8 13.8 + - - +
399C VAL* 3.7 11.1 - - + +
400C LYS 3.5 20.3 + - - -
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Residues in contact with LEU 367 (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 PHE* 5.1 2.2 - - + -
332C VAL* 3.2 26.7 - - + -
333C GLU 3.1 12.1 + - - +
334C ARG* 3.2 15.4 - - + +
335C LYS* 3.0 26.9 + - - +
365C VAL* 3.7 5.8 + - + -
366C TYR* 1.3 71.3 - - - +
368C VAL* 1.3 65.9 + - - +
369C GLU* 4.1 0.6 + - + -
400C LYS* 3.7 7.2 - - + +
402C THR* 3.6 27.8 - - + +
408C SER* 4.5 21.1 - - - +
411C TYR* 3.8 30.1 - - + -
412C LEU* 4.6 15.9 - - + -
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Residues in contact with VAL 368 (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 LYS* 3.8 7.0 - - + +
337C LEU* 4.3 14.1 - - + -
340C LEU* 6.6 0.2 - - + -
366C TYR* 4.1 16.8 - - + +
367C LEU* 1.3 75.7 - - - +
369C GLU* 1.3 69.8 + - - +
371C HIS* 4.3 18.2 - - + +
388C VAL* 5.1 15.5 - - + -
399C VAL* 4.5 13.0 - - + -
400C LYS 3.3 16.7 + - - +
401C ARG* 4.2 4.9 - - + -
402C THR* 2.9 33.3 + - - +
408C SER* 5.5 0.2 - - - -
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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