Contacts of the strand formed by residues 373 - 381 (chain C) in PDB entry 5U0A
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 373 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224C LEU* 2.7 71.5 + - + +
225C GLY 4.5 11.8 + - - +
343C HIS* 4.9 1.3 - - - -
371C SER 4.5 4.9 - - - +
372C LEU* 1.3 79.5 - - - +
374C LEU* 1.3 54.6 + - - +
394C THR* 5.2 7.8 + - - +
395C THR* 3.3 34.5 + - + +
397C ALA* 3.8 26.8 - - - +
400C ARG* 4.7 16.4 - - + +
194N THR 5.1 3.8 - - - +
196N THR* 5.1 6.1 + - - -
218N GLN* 5.0 11.5 - - - +
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Residues in contact with LEU 374 (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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221C TYR* 4.2 19.1 - - + -
222C HIS 3.5 26.0 - - - +
223C PRO* 3.7 12.3 - - + -
224C LEU* 5.0 0.4 - - - +
340C ALA* 3.4 24.0 - - - +
342C LEU* 3.5 33.9 - - + -
343C HIS* 4.1 24.3 - - + +
355C LEU* 4.4 14.8 - - + -
373C ARG* 1.3 74.6 - - - +
375C ARG* 1.3 72.7 + - - +
394C THR* 3.4 2.6 - - - -
395C THR* 3.0 30.0 + - - +
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Residues in contact with ARG 375 (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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56C ASP* 3.4 16.9 + - - -
57C VAL 4.5 2.0 + - - -
58C GLU* 5.5 9.1 - - - +
69C TRP* 3.0 46.5 - - - +
221C TYR* 3.7 0.9 - - - -
222C HIS* 2.8 46.1 + - - +
224C LEU* 3.9 27.7 - - + +
373C ARG 4.0 0.2 + - - -
374C LEU* 1.3 79.0 - - - +
376C ALA* 1.3 69.7 + - - +
377C PHE* 3.2 30.4 - - + -
392C THR* 4.9 2.7 - - - -
393C ALA 3.1 15.7 - - - +
394C THR* 3.5 21.5 - - + +
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Residues in contact with ALA 376 (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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219C VAL* 3.7 14.1 - - + -
220C SER 3.2 11.7 - - - +
221C TYR* 3.7 25.4 - - + -
339C ASP* 4.5 10.5 - - + -
340C ALA* 5.1 2.5 - - - +
375C ARG* 1.3 73.8 - - - +
377C PHE* 1.3 64.2 + - - +
378C GLY 4.0 0.2 - - - -
391C PHE* 3.8 2.7 - - + +
392C THR* 3.3 5.5 - - - -
393C ALA* 2.9 37.5 + - + +
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Residues in contact with PHE 377 (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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59C ILE 5.4 3.1 - - - -
62C PRO* 3.4 29.4 - - + +
65C ALA* 3.4 22.2 - - + -
66C ALA* 4.0 6.5 - - + -
69C TRP* 3.5 24.9 - + - -
191C TYR* 4.4 4.1 + - - -
218C THR 3.8 2.3 - - - +
219C VAL* 3.3 2.1 - - - -
220C SER* 2.9 40.0 + - - +
222C HIS* 4.0 20.2 - + - -
375C ARG* 3.2 41.5 - - + -
376C ALA* 1.3 70.6 - - - +
378C GLY* 1.3 59.4 + - - +
379C PHE 4.3 0.2 + - - -
391C PHE 3.7 1.8 - - - -
392C THR* 3.4 37.0 - - + -
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Residues in contact with GLY 378 (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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62C PRO* 4.7 2.9 - - - +
218C THR 3.8 0.7 - - - -
219C VAL* 3.7 25.2 - - - +
328C ALA* 4.5 0.2 - - - -
376C ALA 4.0 0.6 - - - -
377C PHE* 1.3 75.6 - - - +
379C PHE* 1.3 60.1 + - - -
380C ASP 3.9 2.0 - - - -
390C TRP* 3.1 5.2 - - - +
391C PHE* 2.9 48.3 + - - -
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Residues in contact with PHE 379 (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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63C PRO* 4.7 11.2 - - + -
153C TRP* 4.4 13.2 - + - -
191C TYR* 3.9 37.2 - + + -
217C GLY* 3.2 23.4 - - - -
218C THR 3.4 8.3 + - - -
328C ALA* 3.9 3.5 - - - +
377C PHE 4.3 0.4 + - - -
378C GLY* 1.3 71.9 - - - +
380C ASP* 1.3 62.2 + - - +
381C GLN* 2.7 49.4 - - + -
387C ASP* 3.8 25.8 - - + -
389C GLN 3.7 6.1 - - - -
390C TRP* 3.0 46.0 - + + -
21N PHE* 4.2 7.6 - + - -
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Residues in contact with ASP 380 (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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217C GLY* 4.9 1.1 - - - -
327C PRO* 5.6 1.0 - - - +
328C ALA* 3.0 37.6 + - + +
329C GLU* 3.4 3.3 - - - -
330C ALA* 2.8 31.4 + - + +
378C GLY 3.9 0.8 - - - -
379C PHE* 1.3 72.6 - - - +
381C GLN* 1.3 74.8 + - - +
388C LYS* 3.0 32.4 + - - -
389C GLN 2.8 39.6 + - - +
391C PHE* 5.1 2.6 - - + -
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Residues in contact with GLN 381 (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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191C TYR* 3.8 3.4 - - - -
216C ARG* 2.8 37.6 + - - +
217C GLY* 2.7 36.5 - - - +
327C PRO* 6.0 1.4 - - - +
379C PHE* 2.7 36.9 + - + +
380C ASP* 1.3 83.6 + - - +
382C ASP* 1.3 66.7 + - - +
383C GLY 3.8 0.9 + - - -
386C ARG 3.4 1.8 - - - +
387C ASP* 2.7 40.2 - - - +
388C LYS* 4.0 4.5 - - - +
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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