Contacts of the strand formed by residues 354 - 359 (chain C) in PDB entry 1SZU
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 MET 354 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C VAL* 3.6 45.0 - - + +
209C GLN 4.2 2.0 - - - +
210C GLY* 4.4 1.3 - - - -
214C PHE* 3.6 45.4 - - + +
242C GLN* 4.3 15.7 - - + -
243C SER* 3.9 20.9 - - - -
247C ARG* 3.4 20.5 + - + +
248C THR* 3.9 19.1 - - + -
350C GLY* 3.1 21.7 - - - -
351C LEU 2.9 15.1 + - - +
352C GLY 3.3 0.2 - - - -
353C ALA* 1.3 73.8 - - - +
355C ILE* 1.3 60.1 + - - +
400C LEU* 5.2 0.2 - - + -
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Residues in contact with ILE 355 (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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214C PHE* 3.3 4.9 - - - -
328C GLY* 3.9 22.4 - - - +
331C LEU* 4.2 19.1 - - + -
332C LYS* 4.0 15.7 - - + -
335C LEU* 3.7 29.8 - - + -
348C VAL* 5.4 0.7 - - + -
349C ARG 3.6 6.3 - - - +
350C GLY* 3.7 20.0 - - - -
352C GLY 3.3 25.6 - - - +
353C ALA* 3.1 12.5 + - - +
354C MET* 1.3 78.3 - - - +
356C ALA* 1.3 68.4 + - - +
399C ILE* 2.8 35.5 + - + +
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Residues in contact with ALA 356 (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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213C GLY 4.6 0.7 - - - +
214C PHE* 3.6 30.0 - - + -
335C LEU* 5.6 0.4 - - - -
348C VAL* 3.7 0.2 - - - -
349C ARG* 3.0 39.1 + - - +
355C ILE* 1.3 80.5 - - - +
357C ILE* 1.3 68.5 + - - +
396C VAL* 3.9 13.2 - - + -
397C LEU 3.0 15.9 - - - +
398C ARG* 4.1 1.3 - - - -
399C ILE* 5.8 1.1 - - - -
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Residues in contact with ILE 357 (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 LEU* 3.7 38.6 - - + -
345C ILE* 4.2 15.5 - - + -
347C ASP 3.1 15.0 - - - +
348C VAL* 4.0 14.6 - - + -
349C ARG* 5.1 1.8 - - - +
356C ALA* 1.3 79.3 - - - +
358C GLU* 1.3 59.2 + - - +
359C LEU* 4.0 10.9 + - + -
395C ASN 4.1 0.2 - - - +
396C VAL* 3.4 4.3 - - - +
397C LEU* 2.8 64.2 + - + +
417C ILE* 5.6 1.6 - - + -
421C PHE* 3.9 21.1 - - + -
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Residues in contact with GLU 358 (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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175C LEU* 3.2 14.4 - - - +
176C HIS* 2.9 25.3 + - - -
215C TYR* 2.7 23.1 + - - -
344C GLU 3.7 0.3 - - - +
345C ILE* 3.8 2.8 - - - -
346C GLY* 3.1 24.9 + - - -
347C ASP* 3.2 10.6 + - + -
349C ARG* 3.2 19.6 + - - +
357C ILE* 1.3 75.3 - - - +
359C LEU* 1.3 60.0 + - - +
360C PHE* 3.4 20.4 - - + -
393C TYR* 5.5 0.9 - - - -
395C ASN* 2.9 43.4 + - - +
396C VAL* 3.8 7.6 - - + +
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Residues in contact with LEU 359 (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 GLU 3.2 4.0 - - - +
345C ILE* 3.7 32.5 - - + +
357C ILE* 4.0 10.3 - - + +
358C GLU* 1.3 78.6 - - - +
360C PHE* 1.3 62.2 + - - +
369C ASP* 3.0 32.5 + - + +
372C LEU* 3.7 32.1 - - + +
373C THR* 3.7 27.1 - - - +
376C ILE* 4.5 2.0 - - + -
395C ASN* 2.7 27.0 + - - +
397C LEU* 4.7 7.4 - - + -
421C PHE* 3.8 21.1 - - + -
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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