Contacts of the helix formed by residues 202 - 218 (chain B) in PDB entry 1ZY3
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 ILE 202 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 4.7 16.2 - - + +
71A PRO 5.5 2.0 - - - +
72A GLY* 5.6 3.1 - - - -
77A ARG* 3.7 28.9 - - + +
81A VAL* 4.3 13.9 - - + -
84A GLU* 2.8 12.7 + - - +
201B ILE* 1.3 91.8 - - + +
203B LYS* 1.3 59.4 + - - +
204B ASN* 3.2 4.0 - - + +
205B ILE* 3.2 38.1 + - + +
206B ALA* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 2.7 56.5 + - + +
85A LEU* 3.8 9.9 - - + +
87A GLN* 2.9 24.9 + - - -
88A GLY* 5.1 6.5 - - - +
201B ILE 4.0 2.4 - - - +
202B ILE* 1.3 72.0 - - - +
204B ASN* 1.3 55.6 + - - +
206B ALA* 3.6 1.5 - - - +
207B ARG* 2.7 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 3.2 1.5 - - + -
203B LYS* 1.3 78.4 - - - +
205B ILE* 1.3 81.2 + - + +
207B ARG* 3.4 25.3 + - - +
208B HIS* 3.1 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.6 43.2 - - + +
69A VAL* 6.3 0.4 - - + -
70A THR* 3.3 31.4 - - + +
81A VAL* 3.9 11.0 - - + -
202B ILE* 3.2 42.6 + - + +
204B ASN* 1.3 91.8 - - - +
206B ALA* 1.3 65.1 + - - +
208B HIS* 3.1 20.6 + - + +
209B LEU* 3.3 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.2 24.7 - - + +
84A GLU* 3.6 18.2 - - + -
85A LEU* 3.7 14.1 - - + +
202B ILE 3.0 16.1 + - - +
203B LYS 3.6 4.3 - - - +
205B ILE* 1.3 77.0 - - - +
207B ARG* 1.3 57.3 + - - +
209B LEU* 3.1 17.6 - - - +
210B ALA* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.5 20.3 - - + +
203B LYS* 2.7 26.8 + - - +
204B ASN* 3.6 30.4 + - - +
206B ALA* 1.3 70.6 - - - +
208B HIS* 1.3 61.0 + - - +
210B ALA* 3.9 0.9 - - + -
211B GLN* 2.8 63.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLN* 2.8 38.3 + - + -
67A LEU* 3.7 16.7 - - + +
204B ASN* 3.1 17.3 + - - +
205B ILE* 3.1 14.7 + - + +
207B ARG* 1.3 76.0 - - - +
209B LEU* 1.3 56.8 + - - +
211B GLN* 4.1 3.0 - - - +
212B VAL* 2.9 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.8 28.4 - - + +
67A LEU* 3.7 25.0 - - + +
81A VAL* 3.7 37.7 - - + +
82A SER* 4.8 5.2 - - - -
85A LEU* 5.8 0.9 - - + -
94A ARG* 4.5 3.8 + - - +
97A ALA* 4.8 19.1 - - + -
101A PHE* 4.8 10.1 - - + -
205B ILE 3.3 19.0 + - - +
206B ALA* 3.1 23.1 - - - +
208B HIS* 1.3 78.8 - - - +
210B ALA* 1.3 60.7 + - + +
212B VAL* 4.5 1.1 - - - -
213B GLY* 2.8 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.7 19.1 - - + -
94A ARG* 3.0 43.6 + - - +
206B ALA 3.0 20.0 + - - +
207B ARG* 3.4 5.4 - - + +
208B HIS 3.1 0.2 - - - -
209B LEU* 1.3 79.1 - - + +
211B GLN* 1.3 60.1 + - + +
214B ASP* 2.8 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 2.8 51.4 + - + +
208B HIS* 4.2 3.0 - - - +
210B ALA* 1.3 75.4 - - + +
212B VAL* 1.3 54.5 + - + +
214B ASP* 3.8 5.8 - - - +
215B SER* 2.6 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.8 17.7 - - + -
63A LEU* 4.8 1.1 - - + -
66A GLN* 3.7 34.8 - - - +
208B HIS* 2.9 34.2 + - + +
209B LEU* 4.2 2.5 - - - +
211B GLN* 1.3 77.8 - - + +
213B GLY* 1.3 58.4 + - - +
215B SER* 3.0 5.9 + - - -
216B MET* 2.9 45.1 + - + +
220B ILE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 5.1 7.0 - - - +
56A PHE* 4.6 10.3 - - - -
59A THR* 6.3 0.4 - - - -
63A LEU* 5.5 2.0 - - - -
93A GLY* 5.8 1.8 - - - -
94A ARG* 4.9 2.2 - - - -
209B LEU 2.8 19.0 + - - -
210B ALA 3.8 0.2 - - - -
212B VAL* 1.3 76.4 - - - +
214B ASP* 1.3 59.9 + - - +
216B MET* 4.0 2.9 - - - +
217B ASP* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 2.7 23.5 + - - -
92A TRP* 3.5 16.1 - - + -
93A GLY* 3.1 17.4 - - - -
94A ARG* 2.6 43.2 + - - -
159A ARG* 4.7 1.9 + - - -
210B ALA 2.8 14.2 + - - +
211B GLN* 3.8 5.9 - - - +
213B GLY* 1.3 76.3 - - - +
215B SER* 1.3 62.1 + - - +
217B ASP* 4.1 0.4 - - - +
218B ARG* 3.3 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ARG* 3.2 44.9 + - - +
211B GLN 2.6 23.4 + - - -
212B VAL* 3.0 14.7 + - - -
214B ASP* 1.3 75.5 - - - +
216B MET* 1.3 61.6 + - - +
219B SER 3.2 3.1 + - - -
220B ILE* 2.9 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 3.5 17.6 - - - +
56A PHE* 3.4 71.3 - - + +
57A ARG* 4.3 11.4 - - - +
212B VAL* 2.9 29.1 + - + +
213B GLY 4.0 0.7 - - - +
215B SER* 1.3 76.6 + - - +
217B ASP* 1.3 64.7 + - - +
219B SER* 3.2 12.8 + - - -
220B ILE* 3.5 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 4.2 1.4 - - - +
52A PHE* 3.3 35.3 + - + +
55A ARG* 2.7 58.8 + - - +
92A TRP* 4.5 9.1 - - + -
93A GLY* 5.9 2.3 - - - -
96A VAL* 6.0 3.3 - - - +
153A GLY 3.7 0.5 - - - +
213B GLY 2.9 20.1 + - - +
214B ASP* 4.1 3.1 - - - +
216B MET* 1.3 77.0 - - - +
218B ARG* 1.3 86.6 + - - +
219B SER 2.8 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 3.5 9.1 + - - +
55A ARG* 3.1 14.1 - - - +
92A TRP* 3.5 39.2 - - + -
149A LEU 3.5 20.9 + - - -
150A TYR* 4.7 2.8 - - - +
152A ASP* 2.7 28.5 + - - +
153A GLY* 3.3 16.1 - - - +
155A LEU 4.9 6.4 + - - -
156A GLU* 3.4 40.7 - - + +
159A ARG* 2.9 13.4 + - - +
160A ARG* 4.1 1.2 - - - +
214B ASP 3.3 8.9 + - - +
216B MET 3.4 0.2 - - - -
217B ASP* 1.3 109.2 + - - +
219B SER* 1.3 67.6 + - - +
----------------------------------------------------------
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