Contacts of the strand formed by residues 295 - 305 (chain D) 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 THR 295 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287D ARG* 3.2 28.4 + - - +
288D ASN 3.6 6.0 + - - -
289D LYS* 4.2 11.7 - - - +
293D VAL 4.3 5.8 - - - +
294D THR* 1.3 78.5 - - - +
296D THR* 1.3 69.4 + - - +
297D TRP* 4.1 5.1 + - + +
336D GLU* 3.2 36.5 + - - +
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Residues in contact with THR 296 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286D LEU 3.7 0.6 + - - +
287D ARG* 3.3 6.6 - - - +
288D ASN* 2.9 52.0 + - - +
294D THR* 4.9 9.4 - - + -
295D THR* 1.3 79.4 + - - +
297D TRP* 1.3 69.8 + - - +
298D GLU* 5.8 1.4 - - - +
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Residues in contact with TRP 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ASN* 5.7 2.6 + - - -
285D ASN* 3.8 37.0 - - + -
286D LEU 3.4 3.4 - - - -
287D ARG* 3.5 44.4 - - + -
295D THR* 4.1 7.0 + - + -
296D THR* 1.3 83.4 - - - +
298D GLU* 1.3 62.8 + - - +
299D ARG 4.3 0.2 - - - -
335D CYS* 3.9 12.8 - - + -
336D GLU* 2.9 24.2 + - - -
338D ARG* 3.3 48.1 - - - +
341D CYS* 3.9 19.5 - - - -
354D ILE* 3.9 13.5 - - + -
356D GLN* 3.9 18.4 - - + -
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Residues in contact with GLU 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D ASN* 4.1 3.4 - - - -
286D LEU* 2.9 41.9 + - + +
288D ASN* 6.6 0.2 - - + -
296D THR* 5.8 2.0 - - - +
297D TRP* 1.3 76.4 - - - +
299D ARG* 1.3 65.8 + - - +
300D LEU* 3.3 39.6 + - + +
313D PRO* 5.0 4.0 - - - +
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Residues in contact with ARG 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C HIS* 4.1 24.4 + - - -
141C ASP* 4.6 4.6 + - - -
144C ILE* 3.9 35.1 - - - +
145C ASN* 4.9 12.0 - - - +
171C ARG* 4.6 8.5 - - - +
283D TYR* 3.3 52.8 - - + +
284D LEU 3.5 4.5 - - - +
285D ASN* 3.4 23.6 + - - +
297D TRP 4.3 0.2 - - - -
298D GLU* 1.3 70.8 - - - +
300D LEU* 1.3 69.6 + - - +
314D ARG* 4.1 25.9 + - - +
358D GLU* 5.4 1.8 + - - -
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Residues in contact with LEU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D TYR* 3.4 8.9 - - - -
284D LEU 2.9 31.5 + - - +
286D LEU* 4.0 24.5 - - + -
298D GLU* 3.5 43.1 - - - +
299D ARG* 1.3 84.8 - - - +
301D TYR* 1.3 61.5 + - - +
302D PHE* 3.4 8.2 - - + -
311D CYS* 3.5 31.9 - - - -
312D GLN 4.3 2.0 - - - +
313D PRO* 3.6 27.6 - - + -
314D ARG 5.0 0.7 - - - +
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Residues in contact with TYR 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 2.8 32.0 + - + +
16C SER* 4.0 26.9 - - - -
17C PRO* 3.4 29.4 - - + -
281D ALA* 3.6 24.9 - - + +
282D GLY* 3.6 27.8 - - - -
283D TYR* 3.8 22.4 - + + -
300D LEU* 1.3 73.0 - - - +
302D PHE* 1.3 61.2 + - - +
303D PHE* 4.0 19.5 - + + -
310D MET 3.9 0.2 - - - +
311D CYS* 3.3 4.9 - - - -
312D GLN* 2.9 48.2 + - + +
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Residues in contact with PHE 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D ALA* 3.2 2.9 - - - +
282D GLY 2.9 35.0 + - - +
284D LEU* 3.5 43.3 - - + -
286D LEU* 3.7 17.9 - - + -
300D LEU* 3.4 29.6 - - + -
301D TYR* 1.3 75.2 - - - +
303D PHE* 1.3 61.4 + - - +
309D LEU* 4.3 12.1 - - + -
310D MET 3.3 7.4 - - - -
311D CYS* 3.6 31.4 - - + -
322D ILE* 4.0 22.9 - - + -
353D ILE* 5.8 0.4 - - + -
355D LEU* 3.5 25.6 - - + -
366D TRP* 3.5 10.8 - - + -
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Residues in contact with PHE 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLN* 5.7 1.8 - - - -
279D GLN* 5.9 0.9 - - - +
280D LYS 3.2 7.0 - - - -
281D ALA* 3.6 20.6 - - + -
301D TYR* 4.0 16.2 - + + -
302D PHE* 1.3 79.2 - - - +
304D THR* 1.3 65.1 + - - +
305D GLN* 3.9 26.7 - - + -
309D LEU* 3.9 3.3 - - - +
310D MET* 2.9 68.7 + - + +
312D GLN* 4.1 31.6 - - + -
319D GLY* 4.5 13.7 - - - -
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Residues in contact with THR 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D ILE 4.0 0.2 + - - -
279D GLN* 3.2 37.7 - - - +
280D LYS* 3.0 18.2 + - + +
303D PHE* 1.3 77.8 - - - +
305D GLN* 1.3 61.5 + - - +
306D GLY 4.3 0.2 - - - -
307D GLY 5.4 0.9 - - - -
308D ASN 3.2 7.2 - - - -
309D LEU* 4.1 9.2 - - + -
325D LEU* 4.4 5.6 - - + -
366D TRP* 4.0 17.9 - - + -
369D ALA* 5.5 1.8 - - + -
370D ILE* 4.4 4.0 - - + -
373D ILE* 3.6 29.9 - - + +
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Residues in contact with GLN 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D PHE* 3.7 21.5 + - + -
304D THR* 1.3 75.5 - - - +
306D GLY* 1.3 67.3 + - - +
307D GLY 3.3 0.9 - - - -
308D ASN* 2.8 31.2 + - - +
310D MET* 3.4 36.0 - - + +
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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