Contacts of the strand formed by residues 341 - 348 (chain C) in PDB entry 4X4R
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 VAL 341 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A ARG* 3.6 44.8 + - + +
276A THR* 3.3 31.6 - - + -
316A LEU* 3.9 11.9 - - + -
334A GLN* 3.6 4.3 - - - +
339C SER* 2.9 20.1 + - - -
340C ARG* 1.3 77.6 - - - +
342C PHE* 1.3 62.2 - - - +
365C PHE* 4.1 7.2 - - + -
377C PHE* 4.7 7.2 - - + -
378C GLU 3.4 6.5 - - - +
379C MET* 3.3 25.1 - - - -
380C ARG* 3.3 7.1 + - - -
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Residues in contact with PHE 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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316A LEU* 4.3 5.4 - - - -
334A GLN* 3.7 13.9 - - - +
341C VAL* 1.3 76.0 - - - +
343C ARG* 1.3 69.4 + - - +
344C ARG* 3.7 36.8 - - + -
377C PHE* 3.4 6.4 - - - -
378C GLU* 3.0 72.9 + - + -
379C MET 3.7 14.4 - - - -
380C ARG* 3.6 41.3 - - + +
503C GOL 3.8 27.8 - - - -
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Residues in contact with ARG 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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305A PHE* 5.0 3.8 - - - -
315A PRO 4.7 3.8 + - - -
316A LEU* 2.7 58.4 + - + +
317A ARG* 4.4 0.2 - - - +
334A GLN* 4.6 6.2 - - - +
505A GOL 4.9 0.6 - - - -
342C PHE* 1.3 81.7 - - - +
344C ARG* 1.3 60.2 + - - +
345C MET 4.1 0.9 + - - -
368C PHE* 4.3 15.3 - - + -
370C GLU* 2.8 42.5 + - - -
375C TRP* 3.4 50.8 - - + -
376C ALA 3.3 7.4 - - - +
377C PHE* 4.6 9.4 - - + -
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Residues in contact with ARG 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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342C PHE* 3.7 17.1 + - + -
343C ARG* 1.3 73.3 - - - +
345C MET* 1.3 72.3 + - - +
358C PHE* 4.0 8.3 - - + -
361C ARG* 4.5 0.4 - - - +
375C TRP* 3.4 4.7 - - - -
376C ALA* 2.8 40.0 + - + +
378C GLU* 2.7 46.5 + - + +
503C GOL 2.8 36.6 + - - -
13D U 4.9 5.7 + - - -
14D U 3.6 49.9 + - - +
15D C 4.8 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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343C ARG 4.1 0.2 + - - -
344C ARG* 1.3 84.0 - - - +
346C GLY* 1.3 70.4 + - - +
358C PHE* 3.8 2.3 - - - -
373C ARG* 3.6 24.9 - - - +
375C TRP* 3.5 39.0 - - + -
15D C 3.7 19.7 + - - +
16D G 5.2 1.3 - - - +
17D A 5.9 1.1 - - - +
1H C 3.4 38.1 - - + +
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Residues in contact with GLY 346 (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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344C ARG 3.8 0.6 + - - -
345C MET* 1.3 76.0 - - - +
347C PRO* 1.3 73.8 - - - +
358C PHE* 3.7 14.4 - - - -
373C ARG* 3.2 27.9 + - - -
374C TRP 2.6 22.4 + - - +
15D C 3.8 6.7 - - - -
2H G 3.7 0.5 - - - +
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Residues in contact with PRO 347 (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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346C GLY* 1.3 86.9 - - - +
348C GLN* 1.3 67.7 + - - +
349C PHE 3.7 0.2 + - - -
351C ASP* 4.2 5.8 - - - +
354C ASN* 3.8 13.5 - - + -
355C VAL* 3.7 33.0 - - + +
358C PHE* 3.8 21.5 - - + -
373C ARG* 4.0 1.3 - - - -
374C TRP* 3.1 25.8 + - + -
15D C 3.9 22.9 - - + +
2H G 3.8 15.3 - - + +
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Residues in contact with GLN 348 (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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197A ARG* 3.5 31.5 + - - +
347C PRO* 1.3 76.9 - - - +
349C PHE* 1.3 59.8 + - - +
350C GLU* 3.0 22.7 + - + +
351C ASP* 3.6 18.1 + - - +
355C VAL* 3.5 11.1 - - - +
372C GLY 3.7 5.6 - - - -
373C ARG* 3.8 32.6 - - + +
2H G 4.1 38.0 + - + +
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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