Contacts of the strand formed by residues 297 - 305 (chain C) in PDB entry 5C5B
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 TRP 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285C ASN* 3.9 24.3 - - + +
286C ALA 3.2 4.5 - - - -
287C ARG* 3.6 30.7 - - + +
295C SER* 4.6 3.3 + - - -
296C THR* 1.3 85.0 + - - +
298C ASP* 1.3 62.4 + - - +
299C ARG 3.9 1.7 + - - -
335C CYS* 4.0 16.2 - - - -
336C GLU* 2.8 28.4 + - - -
338C ARG* 3.1 50.8 - - + +
341C CYS* 3.7 21.3 - - - -
354C ILE* 3.9 21.5 - - + -
356C GLN* 3.6 24.2 - - + -
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Residues in contact with ASP 298 (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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284C LEU 3.6 0.7 - - - +
285C ASN* 3.5 3.0 - - - -
286C ALA* 3.1 29.4 + - + +
288C ASN* 3.3 29.1 + - - +
296C THR* 3.0 22.3 + - - -
297C TRP* 1.3 74.5 - - - +
299C ARG* 1.3 63.5 + - - +
300C GLN* 3.5 19.0 + - + +
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Residues in contact with ARG 299 (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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283C TYR* 3.2 53.5 - - + +
284C LEU 3.5 8.3 - - - +
285C ASN* 3.3 20.5 + - - +
297C TRP 3.9 1.8 + - - -
298C ASP* 1.3 72.0 - - - +
300C GLN* 1.3 69.5 + - - +
313C ALA* 4.9 3.8 - - - +
314C ARG* 2.9 34.5 + - - +
140D HIS* 5.3 2.2 - - - -
141D ASP* 4.2 2.4 + - - -
144D MET* 3.6 43.4 - - - +
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Residues in contact with GLN 300 (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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283C TYR* 3.3 9.6 - - - -
284C LEU 2.9 31.7 + - - +
286C ALA* 6.5 0.2 - - + -
288C ASN* 6.0 1.6 - - - +
298C ASP* 3.5 18.3 + - + +
299C ARG* 1.3 80.8 - - - +
301C PHE* 1.3 63.2 + - - +
302C TYR* 3.5 20.5 + - + +
311C SER* 3.3 23.7 + - - +
312C GLN* 3.9 6.6 + - - +
313C ALA* 3.7 33.7 + - + +
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Residues in contact with PHE 301 (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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281C ALA* 3.5 28.7 - - + -
282C GLY* 3.5 26.7 - - - -
283C TYR* 3.6 26.7 - + + -
300C GLN* 1.3 69.9 - - - +
302C TYR* 1.3 60.4 + - - +
303C PHE* 3.6 27.0 - + + -
311C SER* 3.2 2.6 - - - -
312C GLN* 2.8 46.6 + - + +
14D GLN* 3.8 26.7 - - + -
16D SER* 4.2 15.0 - - - -
17D PRO* 3.5 23.1 - - + -
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Residues in contact with TYR 302 (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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281C ALA* 3.3 1.7 - - - +
282C GLY 2.7 42.9 + - - +
284C LEU* 3.7 40.6 - - + -
286C ALA* 3.3 25.3 - - + +
300C GLN* 3.5 31.9 + - + +
301C PHE* 1.3 74.8 - - - +
303C PHE* 1.3 61.1 + - - +
309C LEU* 4.0 30.3 - - + -
310C MET 3.3 3.4 - - - -
311C SER* 3.5 22.4 + - - -
322C ALA* 4.0 13.7 - - + -
353C SER* 5.1 1.7 - - - -
355C LEU* 3.5 22.4 - - + +
366C TRP* 3.7 5.5 - - + -
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Residues in contact with PHE 303 (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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280C LYS 3.4 6.7 - - - +
281C ALA* 3.5 19.5 - - + -
301C PHE* 3.6 30.7 - + + -
302C TYR* 1.3 75.0 - - - +
304C THR* 1.3 68.3 + - - +
305C GLN* 3.6 29.8 - - + -
309C LEU* 4.0 3.7 - - - +
310C MET* 2.8 75.6 + - + +
311C SER 4.3 7.2 - - - -
312C GLN* 4.4 14.1 - - + -
319C GLY* 5.1 8.1 - - - -
366C TRP* 4.4 0.9 - - - -
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Residues in contact with THR 304 (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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278C THR 4.3 0.7 + - - -
279C ARG* 3.5 19.8 - - - +
280C LYS 3.0 35.0 + - - +
303C PHE* 1.3 77.7 - - - +
305C GLN* 1.3 64.4 + - - +
306C GLY 5.0 2.4 + - - -
308C ASN 3.3 8.7 - - - -
309C LEU* 4.4 5.8 - - + +
325C ILE* 4.4 7.6 - - + -
366C TRP* 4.0 16.8 - - + -
369C THR* 4.7 3.6 - - + -
370C ILE* 5.5 2.0 - - + -
373C ILE* 3.7 28.8 - - + +
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Residues in contact with GLN 305 (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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303C PHE* 3.6 27.1 + - + -
304C THR* 1.3 76.3 - - - +
306C GLY* 1.3 64.9 + - - +
307C GLY 3.2 0.3 + - - -
308C ASN* 2.8 32.0 + - - +
310C MET* 3.8 25.2 - - + +
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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