Contacts of the strand formed by residues 275 - 283 (chain D) in PDB entry 3ZXR
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 MET 275 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D ALA* 4.4 7.2 - - + -
133D GLU 3.2 7.6 - - - +
134D ALA* 4.5 0.7 - - - -
242D MET* 4.0 37.7 - - + -
274D GLY* 1.3 73.5 - - - -
276D HIS* 1.3 64.3 + - - +
277D CYS* 3.4 8.8 - - - -
320D THR 5.3 0.2 - - - +
370D PRO* 2.9 40.8 + - + +
371D ASP* 3.5 31.1 - - - +
372D SER* 3.7 16.4 - - - +
376D PRO* 5.1 6.1 - - + -
379D ALA* 4.4 15.7 - - + -
380D PHE* 3.9 25.4 - - + -
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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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131D GLY 3.6 1.2 - - - +
132D ALA* 3.3 6.1 - - - -
133D GLU* 3.0 50.4 + - + +
135D GLU* 4.6 4.0 + - - -
274D GLY* 4.7 1.1 - - - -
275D MET* 1.3 74.0 - - - +
277D CYS* 1.3 59.5 + - - +
278D HIS 4.0 0.7 - - - -
329D ARG* 4.2 2.9 - - - -
366D GLU* 3.0 16.1 + - + +
367D PHE 3.6 6.1 - - - +
368D ARG* 3.4 40.0 + - + +
502D MG 4.3 2.2 - - - -
503D MG 2.5 20.8 - - - -
505D P3S 2.7 63.5 + - + +
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Residues in contact with CYS 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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130D PHE* 4.6 5.4 - - + -
131D GLY 3.5 3.6 - - - +
132D ALA* 4.7 3.6 - - - -
275D MET* 3.4 22.2 - - - -
276D HIS* 1.3 73.4 - - - +
278D HIS* 1.3 62.2 + - - +
279D GLN* 3.1 25.7 + - + +
365D LEU 3.6 0.9 - - - +
367D PHE 2.9 37.2 + - - +
370D PRO* 4.3 0.9 - - - -
380D PHE* 3.7 22.4 - - - -
383D MET* 3.6 30.7 - - - -
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Residues in contact with HIS 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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130D PHE* 3.4 6.4 - - - -
131D GLY 2.7 36.9 + - - +
133D GLU* 2.9 27.9 + - - -
276D HIS 4.5 1.8 - - - -
277D CYS* 1.3 71.3 - - - +
279D GLN* 1.3 60.2 + - - +
352D ARG* 4.5 1.6 - - - -
354D PRO* 4.2 10.0 - - + +
364D ARG* 3.1 36.6 + - + +
365D LEU 3.2 5.6 - - - -
366D GLU* 3.4 23.6 + - + +
501D IQ1 3.4 41.1 - - + +
506D PO4 3.2 24.8 + - - -
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Residues in contact with GLN 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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129D TYR 3.4 2.9 - - - +
130D PHE* 3.7 29.1 - - + -
277D CYS* 3.1 19.1 + - - +
278D HIS* 1.3 79.4 - - - +
280D SER* 1.3 61.2 + - - +
289D MET* 3.8 3.7 - - - +
305D TYR* 2.8 42.5 + - + +
309D LEU* 4.4 0.9 - - - +
364D ARG* 3.2 18.9 - - - +
365D LEU* 2.9 31.8 + - + +
367D PHE* 3.3 23.4 - - - +
383D MET* 3.6 27.0 - - - +
501D IQ1 4.2 0.9 - - - -
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Residues in contact with SER 280 (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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127D THR 3.9 0.2 - - - +
128D ALA* 3.5 3.6 - - - -
129D TYR* 2.9 35.6 + - - +
279D GLN* 1.3 76.9 - - - +
281D LEU* 1.3 64.6 + - - +
282D TRP* 3.0 25.3 + - - -
289D MET* 3.6 22.2 - - - -
305D TYR* 6.2 0.7 - - - -
361D LYS 6.0 0.2 - - - -
363D LYS 4.0 9.2 - - - -
364D ARG* 4.1 0.2 - - - -
501D IQ1 3.0 24.8 + - - -
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Residues in contact with LEU 281 (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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119D LEU* 4.3 8.5 - - + -
124D ILE* 4.2 15.3 - - + -
125D ALA* 3.8 9.9 - - + -
127D THR 3.4 2.9 - - - +
128D ALA* 3.7 29.2 - - + -
280D SER* 1.3 75.1 - - - +
282D TRP* 1.3 68.9 + - - +
288D LEU* 3.1 33.3 + - + +
289D MET* 3.4 15.4 - - - +
301D THR* 4.5 5.8 - - + -
305D TYR* 3.9 19.3 - - + +
384D LEU* 3.9 15.5 - - + -
388D LEU* 4.2 4.9 - - + -
391D ILE* 3.6 31.4 - - + -
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Residues in contact with TRP 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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125D ALA* 3.3 4.1 - - - +
126D ASP* 2.9 25.0 + - - +
127D THR* 2.9 22.0 + - - +
129D TYR* 3.4 36.0 - + + -
232D PHE* 5.8 4.9 - + - -
280D SER* 3.0 26.6 + - - -
281D LEU* 1.3 93.3 - - - +
283D LYS* 1.3 60.3 + - - +
285D GLY* 3.6 26.7 - - - +
286D ALA 3.4 16.8 - - - +
287D PRO* 3.7 24.0 - - + +
288D LEU* 4.3 1.8 - - - -
289D MET* 5.6 0.2 - - - +
361D LYS* 3.6 53.2 + - + -
501D IQ1 5.2 6.4 + + - -
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Residues in contact with LYS 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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123D GLY* 2.7 37.7 + - - +
124D ILE 4.2 6.5 - - - +
125D ALA* 4.1 12.8 - - - +
126D ASP* 3.5 12.6 - - - +
282D TRP* 1.3 74.1 - - - +
284D ASP* 1.3 85.3 + - - +
285D GLY 3.1 1.6 - - - -
286D ALA* 2.9 30.8 + - - +
288D LEU* 4.1 17.6 - - + +
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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