Contacts of the strand formed by residues 271 - 279 (chain D) in PDB entry 5E6J
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 271 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D ASN* 5.7 1.8 - - - -
163D LEU* 4.1 14.1 - - + -
267D GLY* 3.6 2.9 - - - -
268D ASN* 2.7 30.8 + - - +
270D GLN* 1.3 93.4 - - + +
272D GLY* 1.3 68.0 + - - +
74E ARG 3.4 7.8 + - - -
76E AYE 6.0 0.2 - - - -
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Residues in contact with GLY 272 (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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265D TYR* 3.6 17.5 - - - -
266D THR 2.9 15.3 - - - -
267D GLY* 3.9 2.2 - - - -
271D CYS* 1.3 82.8 - - - +
273D HIS* 1.3 60.7 + - - -
74E ARG 3.0 8.5 + - - -
76E AYE 2.8 26.7 + - - -
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Residues in contact with HIS 273 (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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107D TRP* 3.2 44.6 + + - -
112D CYS* 4.3 4.0 - - + +
264D GLU* 3.7 2.4 - - - +
265D TYR* 3.6 3.8 - - - -
266D THR* 2.7 53.0 + - - +
272D GLY* 1.3 73.5 + - - +
274D TYR* 1.3 82.5 + - - +
275D THR* 3.5 13.6 + - + -
287D ASP* 2.6 29.2 + - - -
76E AYE 4.2 5.1 - - - +
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Residues in contact with TYR 274 (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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112D CYS* 3.6 25.2 - - + +
113D TYR* 3.5 23.6 - - + -
116D SER* 3.7 13.2 - - - +
164D GLY 3.5 20.0 - - - -
165D ASP* 3.2 24.3 + - - -
166D VAL* 3.3 24.3 + - + +
263D ASN* 4.2 13.0 - - + -
264D GLU 3.5 10.8 - - - -
265D TYR* 3.7 24.2 - + + -
273D HIS* 1.3 84.4 + - - +
275D THR* 1.3 69.1 + - - +
287D ASP* 4.0 1.9 - - - +
302D THR* 3.6 24.0 - - + +
303D ASP* 4.3 0.9 + - - -
73E LEU* 3.2 14.7 - - + +
75E GLY* 4.1 7.9 - - - -
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Residues in contact with THR 275 (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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116D SER* 4.3 5.6 - - - -
263D ASN* 3.8 1.6 - - - +
264D GLU* 2.6 68.6 + - - +
273D HIS* 3.5 11.2 - - + -
274D TYR* 1.3 80.7 - - - +
276D HIS* 1.3 60.4 + - - +
277D ILE 4.0 0.2 + - - -
285D ARG* 3.2 22.4 + - - +
286D ILE 3.6 10.3 - - - -
287D ASP* 3.5 30.5 - - + +
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Residues in contact with HIS 276 (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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102D LEU* 5.3 0.4 - - + -
116D SER* 4.0 15.2 + - - +
119D LEU* 3.5 39.6 - - + +
120D ALA* 3.8 15.7 - - + -
123D GLN* 2.9 26.5 + - - -
261D CYS* 3.7 29.2 - - + +
262D ALA 3.5 5.0 + - - -
263D ASN* 3.0 27.0 + - - -
275D THR* 1.3 73.1 - - - +
277D ILE* 1.3 60.5 + - - +
278D THR* 4.0 9.8 - - + -
284D TYR 3.8 0.2 - - - +
285D ARG* 3.4 3.8 - - - +
286D ILE* 2.7 45.5 + - + +
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Residues in contact with ILE 277 (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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254D LEU* 3.7 22.0 - - + -
259D PHE* 3.7 5.2 - - + -
261D CYS* 3.3 1.9 - - - +
262D ALA 2.7 43.7 + - - +
264D GLU* 3.9 16.2 - - + +
275D THR 4.3 4.9 - - - +
276D HIS* 1.3 79.4 - - - +
278D THR* 1.3 65.7 + - - +
283D LEU* 4.3 19.5 - - + -
284D TYR 3.3 10.1 - - - +
285D ARG* 4.3 15.5 - - + -
294D MET* 5.7 1.3 - - - -
297D TYR* 3.3 52.0 - - + -
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Residues in contact with THR 278 (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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100D GLY 6.0 0.9 - - - +
102D LEU* 4.7 9.8 - - + +
123D GLN* 2.7 41.4 + - - +
259D PHE* 5.1 1.1 - - - -
260D LEU 3.7 1.2 + - - -
261D CYS* 3.8 4.7 - - - -
276D HIS* 4.0 8.7 - - + -
277D ILE* 1.3 76.8 - - - +
279D ALA* 1.3 72.4 + - - +
280D LYS* 4.2 10.2 - - + +
283D LEU* 3.7 6.2 - - - +
284D TYR* 2.8 53.9 + - + +
286D ILE* 4.7 8.5 - - + -
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Residues in contact with ALA 279 (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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256D GLN* 4.9 9.0 - - + -
257D GLY 5.3 1.8 - - - +
259D PHE* 4.0 20.6 - - + +
260D LEU* 3.3 20.3 + - - +
278D THR* 1.3 80.7 + - - +
280D LYS* 1.3 66.4 + - - +
282D THR 3.5 5.2 - - - +
283D LEU* 4.0 19.1 - - + -
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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