Contacts of the strand formed by residues 281 - 289 (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 ALA 281 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C GLU* 3.4 10.8 - - - +
279D GLN* 3.9 12.1 - - - +
280D LYS* 1.3 85.2 + - - +
282D GLY* 1.3 58.4 + - - +
301D TYR* 3.6 19.5 - - + +
302D PHE 3.2 5.8 - - - +
303D PHE* 3.6 18.6 - - + -
366D TRP* 4.1 3.8 - - - -
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Residues in contact with GLY 282 (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* 3.9 5.2 - - - -
281D ALA* 1.3 75.8 - - - +
283D TYR* 1.3 63.8 + - - -
284D LEU* 3.7 0.6 + - - -
301D TYR* 3.6 21.0 - - - -
302D PHE* 2.9 32.2 + - - +
362D GLU* 5.1 6.5 - - - -
366D TRP* 3.9 8.4 - - - -
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Residues in contact with TYR 283 (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 3.6 15.0 - - - -
15C ASP* 2.4 36.8 + - + -
17C PRO* 3.5 9.9 - - + +
282D GLY* 1.3 71.6 - - - -
284D LEU* 1.3 71.2 + - - +
299D ARG* 3.3 57.6 + - + +
300D LEU* 3.4 18.2 - - - -
301D TYR* 3.8 28.0 - + + -
314D ARG* 3.2 35.0 + - + -
356D GLN 4.7 0.5 - - - +
357D ALA* 5.2 0.2 - - - -
362D GLU* 3.9 15.0 + - - +
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Residues in contact with LEU 284 (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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282D GLY 3.7 1.7 + - - +
283D TYR* 1.3 82.6 - - - +
285D ASN* 1.3 65.7 + - - +
286D LEU 3.8 0.3 + - - -
298D GLU 3.6 0.2 - - - +
299D ARG* 3.5 3.0 - - - +
300D LEU 2.9 31.7 + - - +
302D PHE* 3.5 32.1 - - + -
309D LEU* 6.1 0.4 - - + -
342D PHE* 3.8 21.8 - - + -
355D LEU* 4.1 16.2 - - + -
356D GLN 3.5 17.0 - - - +
357D ALA* 4.0 13.9 - - + -
362D GLU* 4.2 1.3 - - - +
366D TRP* 3.5 47.1 - - + +
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Residues in contact with ASN 285 (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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144C ILE* 6.1 0.2 - - - +
145C ASN* 5.1 5.8 + - - +
148C SER* 2.6 33.5 + - - -
284D LEU* 1.3 72.5 - - - +
286D LEU* 1.3 61.6 + - - +
287D ARG 3.8 0.2 + - - -
297D TRP* 3.8 17.3 - - + -
298D GLU 3.5 3.1 - - - +
299D ARG* 3.4 35.4 + - - +
338D ARG* 4.3 1.7 - - - +
354D ILE 3.7 0.7 - - - +
355D LEU* 3.2 9.3 - - - -
356D GLN* 3.0 58.5 + - + +
357D ALA 5.8 0.8 + - - -
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Residues in contact with LEU 286 (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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284D LEU 3.8 1.2 + - - -
285D ASN* 1.3 71.4 - - - +
287D ARG* 1.3 81.5 + - - +
288D ASN* 3.8 15.3 + - + +
296D THR 3.7 0.5 - - - +
297D TRP* 3.4 3.6 - - - -
298D GLU* 2.9 42.1 + - + +
300D LEU* 4.0 15.9 - - + -
302D PHE* 3.7 22.9 - - + -
311D CYS* 5.7 0.4 - - - -
322D ILE* 5.0 7.9 - - + -
353D ILE* 3.5 36.1 - - + -
355D LEU* 3.7 8.3 - - + -
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Residues in contact with ARG 287 (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 3.8 1.2 + - - -
286D LEU* 1.3 86.5 - - - +
288D ASN* 1.3 59.7 + - - +
289D LYS* 3.8 41.5 + - - +
295D THR* 3.2 23.7 + - - +
296D THR 3.3 6.3 - - - +
297D TRP* 3.5 36.1 - - + -
335D CYS* 3.7 13.5 - - - -
336D GLU* 3.3 16.1 + - - +
353D ILE* 5.9 1.0 - - - +
354D ILE* 3.1 54.9 + - + +
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Residues in contact with ASN 288 (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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286D LEU* 3.8 14.3 + - + +
287D ARG* 1.3 74.7 - - - +
289D LYS* 1.3 62.7 + - - +
290D THR* 4.1 14.9 + - - -
295D THR* 3.6 2.7 - - - -
296D THR* 2.9 49.4 + - - +
298D GLU* 6.6 0.2 - - + -
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Residues in contact with LYS 289 (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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287D ARG* 3.8 41.2 + - - +
288D ASN* 1.3 76.2 + - - +
290D THR* 1.3 59.8 + - - +
291D GLY 3.2 25.7 - - - +
292D LEU* 3.3 27.7 + - - +
293D VAL* 3.3 14.8 + - - +
294D THR 3.3 20.6 - - - +
295D THR* 4.2 4.8 - - - +
336D GLU* 5.6 0.6 + - - -
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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