Contacts of the strand formed by residues 316 - 321 (chain C) in PDB entry 1SA0
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 CYS 316 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C ASN* 4.1 17.9 - - - -
258C ASN* 5.1 4.9 - - - -
259C LEU* 3.9 16.6 - - + -
315C CYS* 1.3 75.0 - - - +
317C LEU* 1.3 61.7 + - - +
318C LEU* 3.7 19.7 - - + -
351C PHE* 5.3 0.2 - - - -
352C LYS* 3.7 27.1 - - - +
377C MET* 2.8 32.2 - - - +
378C LEU* 2.9 29.5 + - + +
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Residues in contact with LEU 317 (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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292C THR* 4.2 12.1 - - + -
295C CYS* 5.0 4.5 - - + -
296C PHE* 5.2 2.9 - - + -
316C CYS* 1.3 81.8 - - - +
318C LEU* 1.3 62.1 - - - +
319C TYR* 3.4 35.0 - - + +
332C ILE* 4.2 25.8 - - + -
351C PHE* 4.4 12.5 - - + -
352C LYS 3.2 10.1 + - - +
353C VAL* 3.5 11.3 - - + +
354C GLY* 2.9 27.2 + - - +
375C VAL* 4.1 11.7 - - + -
377C MET* 3.5 36.3 - - + +
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Residues in contact with LEU 318 (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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237C SER* 3.6 24.8 - - - +
238C ILE* 4.1 7.0 - - - +
241C SER* 3.9 19.1 - - - +
248C LEU* 4.6 14.4 - - + -
249C ASN* 4.3 16.2 - - - +
255C PHE* 5.1 2.2 - - + -
316C CYS* 3.7 32.5 - - + -
317C LEU* 1.3 73.1 - - - +
319C TYR* 1.3 63.9 + - - +
320C ARG* 5.3 1.6 - - - +
352C LYS 5.4 0.2 - - - +
354C GLY* 3.5 3.8 - - - -
374C ALA 4.0 0.3 - - - +
375C VAL 3.4 1.7 - - - -
376C CYS* 2.8 39.9 + - + +
377C MET 3.7 7.5 - - - +
378C LEU* 4.3 20.6 - - + +
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Residues in contact with TYR 319 (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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288C VAL* 4.6 9.4 - - + -
291C ILE* 5.1 2.0 - - + -
292C THR* 2.9 26.8 + - - +
317C LEU* 3.4 39.0 - - + +
318C LEU* 1.3 76.5 - - - +
320C ARG* 1.3 67.2 + - - +
323C VAL* 4.2 15.0 - - + -
328C VAL* 3.7 42.7 + - + +
353C VAL* 4.1 11.0 - - + -
354C GLY 2.8 17.5 + - - +
355C ILE* 3.8 16.6 - - + -
356C ASN* 3.1 22.0 + - - +
374C ALA 3.4 6.5 - - - -
375C VAL* 3.7 34.3 - - + +
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Residues in contact with ARG 320 (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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23C LEU* 5.4 0.6 - - - +
27C GLU* 2.7 34.3 + - - +
233C GLN* 5.7 4.8 - - - +
236C SER* 2.6 29.7 + - - -
237C SER* 4.0 29.5 + - - +
240C ALA* 4.5 12.5 - - + +
244C PHE* 4.3 2.2 - - - -
272C TYR* 5.9 0.4 + - - -
318C LEU 5.3 1.6 - - - +
319C TYR* 1.3 79.7 - - - +
321C GLY* 1.3 59.4 + - - +
323C VAL* 4.7 2.8 - - - +
355C ILE* 5.4 0.4 - - - -
356C ASN* 3.7 20.7 - - + +
358C GLU* 3.6 27.9 + - - +
359C PRO 3.8 8.7 + - - -
360C PRO* 4.0 27.3 - - + +
361C THR 4.7 1.2 + - - +
373C ARG* 3.4 5.7 - - - +
374C ALA* 2.8 40.9 + - + +
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Residues in contact with GLY 321 (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* 1.3 75.0 - - - +
322C ASP* 1.3 61.3 + - - -
323C VAL* 3.1 11.0 + - - +
355C ILE* 4.8 1.4 - - - +
356C ASN 3.3 11.9 + - - -
357C TYR* 3.4 37.3 + - - +
358C GLU 3.7 1.4 + - - -
359C PRO* 4.0 14.8 - - - -
372C GLN 4.0 7.4 - - - -
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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