Contacts of the helix formed by residues 81 - 92 (chain D) in PDB entry 2UZ1
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 81 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D GLU 4.5 6.5 - - - +
54D GLY* 5.6 0.7 - - - -
72D VAL* 4.2 22.0 - - + -
77D GLY 3.4 8.9 + - - +
78D PHE* 2.9 14.7 + - + +
80D ASN* 1.3 76.9 - - - +
82D VAL* 1.3 64.1 + - - +
83D THR 3.4 2.0 - - - -
84D PRO* 3.1 13.9 - - + +
85D ILE* 3.1 25.2 + - + +
97D PHE* 4.5 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C THR* 4.0 19.5 - - - +
82C VAL* 4.4 12.1 - - + -
121C MET* 3.2 35.0 - - + -
78D PHE* 3.8 41.7 - - + +
79D THR* 3.3 14.8 + - - +
80D ASN 3.4 0.4 - - - -
81D ALA* 1.3 75.4 - - - +
83D THR* 1.3 60.7 + - - +
85D ILE* 3.1 9.8 + - + +
86D ALA* 2.9 27.4 + - - +
121D MET* 4.9 2.9 - - + +
125D ILE* 4.0 3.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C THR* 2.7 34.4 + - - +
80C ASN* 2.7 26.9 + - - +
51D ALA* 5.7 2.5 - - - -
55D HIS* 3.8 15.5 - - + +
79D THR 5.0 0.2 + - - -
80D ASN 4.8 1.9 + - - -
82D VAL* 1.3 76.3 - - - +
84D PRO* 1.4 65.3 - - - +
86D ALA* 3.2 3.3 + - - +
87D ASN* 2.8 28.4 + - - +
418D LEU* 4.2 2.9 - - + -
420D SER* 3.5 29.4 - - - +
423D VAL* 4.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ALA* 3.3 36.1 - - + +
54D GLY* 3.6 21.1 - - - -
55D HIS* 3.3 15.7 - - + +
58D GLU* 3.3 22.4 - - - +
80D ASN 4.2 1.1 - - - +
81D ALA* 3.1 19.1 - - - +
83D THR* 1.4 93.8 - - - +
85D ILE* 1.3 63.3 + - - +
87D ASN 3.2 0.3 + - - -
88D ALA* 2.8 24.6 + - - +
97D PHE* 3.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D PHE* 4.0 27.8 - - + -
81D ALA* 3.1 19.9 + - + +
82D VAL* 3.1 15.7 + - + +
84D PRO* 1.3 76.4 - - - +
86D ALA* 1.3 57.1 + - - +
88D ALA 3.3 0.2 + - - -
89D TRP* 2.8 27.5 + - - +
97D PHE* 3.7 35.9 - - + -
122D ALA* 4.6 5.8 - - + -
125D ILE* 3.3 32.5 - - + +
126D THR* 3.5 17.0 - - + -
156D PRO* 3.6 8.1 - - + +
158D LEU* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C THR* 4.0 22.7 - - + -
116C ILE* 4.1 15.5 - - + -
82D VAL 2.9 16.5 + - - +
83D THR 3.7 3.4 - - - +
85D ILE* 1.3 76.6 - - - +
87D ASN* 1.3 63.0 + - - +
89D TRP* 3.3 8.9 + - - +
90D LEU* 3.1 28.4 + - - +
125D ILE* 3.9 13.0 - - + +
418D LEU* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D HIS* 4.4 3.4 - - + -
58D GLU* 2.9 25.0 - - - +
62D ARG* 4.8 5.0 + - - -
83D THR 2.8 21.9 + - - +
84D PRO* 3.7 2.0 - - + +
86D ALA* 1.3 75.6 - - - +
88D ALA* 1.3 57.9 + - - +
90D LEU* 3.4 1.2 + - - +
91D ASP* 3.0 50.6 + - - +
415D HIS* 5.5 1.2 - - - +
416D GLY 5.0 4.9 - - - +
418D LEU* 3.5 33.6 - - + +
419D GLY 4.8 1.4 - - - +
420D SER* 4.7 4.4 - - - +
423D VAL* 4.2 28.3 - - + +
427D THR* 5.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLU* 3.5 18.3 + - + -
84D PRO 2.8 17.3 + - - +
85D ILE 3.8 3.1 - - - +
87D ASN* 1.3 74.9 - - - +
89D TRP* 1.3 57.6 + - - +
92D ARG* 2.9 25.6 + - - -
93D THR* 3.0 38.1 + - - +
95D VAL* 4.3 5.2 - - + -
97D PHE* 4.6 1.8 - - + -
156D PRO* 3.7 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C GLY 4.5 6.9 + - - -
116C ILE* 4.4 3.1 - - + -
85D ILE 2.8 8.5 + - - +
86D ALA 3.3 9.0 - - - +
88D ALA* 1.3 79.4 - - - +
90D LEU* 1.3 84.7 + - + +
91D ASP 3.3 0.2 + - - -
92D ARG* 3.4 12.6 + - - +
124D PRO 3.7 18.4 + - - -
125D ILE* 3.3 48.5 - - + +
126D THR* 3.3 30.5 - - - -
127D LYS* 3.5 16.4 - - + -
155D GLY* 5.6 1.0 - - - -
156D PRO* 3.5 14.9 - - + +
279D ARG* 5.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASN* 6.1 0.9 - - - +
114C ALA 3.6 25.6 - - - +
115C GLY* 4.7 7.0 - - - +
116C ILE* 3.8 18.4 - - + -
86D ALA 3.1 11.0 + - - +
87D ASN 4.3 1.8 - - - +
89D TRP* 1.3 101.0 - - + +
91D ASP* 1.3 60.4 + - - +
92D ARG 3.4 0.2 - - - -
279D ARG* 2.9 32.4 + - - +
417D TYR* 4.0 29.3 - - + -
418D LEU* 3.8 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D GLU* 4.5 1.2 - - - +
62D ARG* 4.1 21.1 + - - +
87D ASN* 3.0 40.2 + - - +
88D ALA 4.0 0.2 - - - +
90D LEU* 1.3 81.2 - - - +
92D ARG* 1.3 69.7 + - - +
93D THR* 3.3 16.9 + - - +
213D SER* 3.6 9.0 + - - -
217D ARG* 3.1 16.1 + - - +
240D GLU* 5.1 2.8 - - - +
279D ARG* 4.5 3.1 - - - +
414D CYS 4.8 0.3 - - - +
416D GLY* 3.3 33.0 + - - -
417D TYR 3.9 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ALA 2.9 6.4 + - - -
89D TRP 3.4 8.2 + - - +
90D LEU 3.4 1.0 - - - -
91D ASP* 1.3 79.1 - - - +
93D THR* 1.3 57.2 + - - +
153D PRO* 3.5 21.9 - - + +
154D ARG* 3.0 33.5 - - - +
155D GLY* 4.4 0.2 - - - -
213D SER* 3.9 12.1 - - - +
214D GLU* 3.9 24.5 - - - +
217D ARG* 2.9 21.1 + - - +
277D GLY 4.0 10.5 + - - -
279D ARG* 3.7 36.9 - - - +
302D ASP* 2.8 42.8 + - - -
304D ASP* 3.7 12.1 + - - +
307D GLU* 3.5 19.8 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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