Contacts of the helix formed by residues 295 - 308 (chain B) in PDB entry 2Z1Z
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 PRO 295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286B LYS 5.0 6.3 - - - +
288B LEU 3.7 8.1 - - - +
289B LEU* 3.9 13.9 - - + -
293B GLY 3.6 4.9 - - - +
294B PHE* 1.4 107.3 - - + +
296B VAL* 1.3 68.8 + - - +
297B ALA* 4.5 4.9 - - + +
298B LYS* 3.1 37.3 + - + +
299B ASP 3.5 0.3 + - - -
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B MET* 3.8 16.7 - - + +
233B ILE* 4.2 8.3 - - + -
263B MET* 3.5 32.3 - - + -
284B ILE* 4.3 3.1 - - + -
288B LEU* 3.0 39.1 + - + +
289B LEU 4.0 9.0 - - - -
290B TYR* 3.9 35.2 - - + +
294B PHE 3.4 0.6 + - - -
295B PRO* 1.3 70.1 - - - +
297B ALA* 1.3 61.4 + - - +
299B ASP* 2.9 15.9 + - - +
300B PHE* 3.1 10.4 + - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASP* 6.0 1.1 - - - +
123B PHE* 4.0 14.0 - - + -
284B ILE* 3.8 34.4 - - + +
285B PRO 4.7 5.4 - - - +
286B LYS* 5.8 2.9 - - + -
288B LEU 4.7 0.6 + - - -
295B PRO* 3.1 5.6 + - + -
296B VAL* 1.3 77.7 - - - +
298B LYS* 1.3 51.6 + - + +
300B PHE* 3.4 7.9 + - - +
301B ASN* 2.7 35.4 + - - +
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B PHE* 3.6 29.5 - - + -
295B PRO* 3.1 28.1 + - + +
297B ALA* 1.3 74.8 - - + +
299B ASP* 1.3 67.0 + - - +
301B ASN* 3.3 6.6 + - - +
302B ARG* 3.1 21.5 + - - +
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Residues in contact with ASP 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 2.8 56.3 + - - +
27A ASN* 4.6 0.7 + - - +
30A MET* 3.5 27.3 - - + +
138B MET* 3.7 18.8 - - + +
290B TYR* 3.5 11.5 + - + -
294B PHE* 3.2 9.6 - - - -
295B PRO 3.5 1.8 + - - -
296B VAL 2.9 9.1 + - - +
298B LYS* 1.3 76.5 - - - +
300B PHE* 1.3 63.7 + - - +
302B ARG* 3.1 7.6 + - - +
303B ILE* 3.0 23.4 + - - +
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PHE* 3.7 22.7 - + + -
131B ASP* 4.4 7.6 - - - -
134B ARG* 4.1 14.1 - - + -
135B LEU* 3.5 44.4 - - + -
138B MET* 3.4 17.2 - - + -
282B THR* 3.1 34.5 - - + -
284B ILE* 3.5 26.0 - - + -
296B VAL 3.1 6.3 + - - +
297B ALA 3.5 7.9 - - - +
299B ASP* 1.3 75.2 - - - +
301B ASN* 1.3 61.8 + - - +
303B ILE* 3.3 5.0 + - + +
304B ILE* 3.0 48.6 + - + +
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Residues in contact with ASN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO* 6.2 0.8 - - - +
98B GLN* 4.1 16.2 + - - +
123B PHE* 3.6 23.5 - - + -
297B ALA 2.7 21.1 + - - +
298B LYS* 3.7 8.1 - - - +
299B ASP 3.2 0.4 - - - -
300B PHE* 1.3 72.6 - - - +
302B ARG* 1.3 59.4 + - - +
304B ILE* 3.4 4.5 + - - +
305B CYS* 3.0 46.6 + - - +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A MET* 3.8 20.2 - - + -
33A LEU* 3.7 26.9 - - + +
34A GLN 5.4 0.4 - - - +
35A ALA 2.9 23.4 + - - -
36A GLY* 3.4 10.6 + - - -
37A TYR* 3.1 26.1 - - - +
157A ASP* 3.1 32.9 + - - +
161A ILE* 4.6 1.3 - - + +
175A TYR* 5.4 1.4 + - - -
298B LYS 3.1 13.6 + - - +
299B ASP* 3.1 10.3 + - - +
301B ASN* 1.3 77.1 - - - +
303B ILE* 1.3 54.9 + - - +
305B CYS* 3.4 4.2 + - - +
306B THR* 2.7 69.3 + - + +
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Residues in contact with ILE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A MET* 3.9 13.5 - - + -
161A ILE* 3.8 39.5 - - + -
134B ARG* 3.8 40.4 - - + +
137B VAL* 4.0 12.8 - - + -
138B MET* 3.8 22.9 - - + +
299B ASP 3.0 19.6 + - - +
300B PHE* 3.6 10.1 - - + +
302B ARG* 1.3 66.1 - - - +
304B ILE* 1.3 68.8 + - + +
305B CYS 3.0 1.7 + - - -
306B THR 3.2 0.5 + - - -
307B CYS* 2.9 35.4 + - + +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 3.4 38.7 - - + +
98B GLN* 4.0 7.6 - - - +
123B PHE* 4.8 9.9 - - + -
124B VAL 5.8 0.9 - - - +
125B SER* 5.8 2.9 - - - -
131B ASP* 5.5 2.5 - - - +
134B ARG* 3.2 39.3 - - + +
300B PHE* 3.0 50.2 + - + +
301B ASN* 3.9 7.2 - - - +
303B ILE* 1.3 77.1 - - - +
305B CYS* 1.3 59.9 + - - +
306B THR 3.6 0.2 + - - -
308B PHE* 3.2 39.8 - - + +
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Residues in contact with CYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 3.2 13.2 - - + -
40A PRO* 3.6 32.8 - - + -
129A LYS* 2.6 28.8 + - - -
97B GLU* 3.5 20.5 - - - +
98B GLN* 5.9 1.1 - - - -
301B ASN* 3.0 35.2 + - - +
302B ARG* 3.8 7.4 - - - +
303B ILE 3.0 0.8 - - - -
304B ILE* 1.3 82.4 - - - +
306B THR* 1.3 58.6 + - + +
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 3.8 22.7 - - + -
129A LYS* 3.4 24.0 - - - +
133A SER* 4.4 2.6 + - - -
154A ALA* 4.2 13.7 + - - +
157A ASP* 4.0 10.5 - - - +
158A SER* 4.7 1.7 + - - -
161A ILE* 3.7 21.5 - - + +
302B ARG* 2.7 65.1 + - + +
303B ILE 3.2 0.8 + - - +
305B CYS* 1.3 79.7 - - - +
307B CYS* 1.3 57.6 + - - +
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Residues in contact with CYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LYS 3.8 7.9 - - - +
130A CYS* 3.8 17.2 - - - +
133A SER* 3.3 31.9 - - - +
158A SER* 5.2 3.8 - - - -
161A ILE* 3.8 24.9 - - - -
134B ARG* 4.4 11.5 + - + -
137B VAL* 5.2 5.2 - - + -
303B ILE* 2.9 31.1 + - + +
306B THR* 1.3 89.1 - - - +
308B PHE* 1.3 59.2 + - - +
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASP* 3.7 16.8 - - - -
129A LYS* 2.8 23.2 - - - +
130A CYS* 3.9 7.4 - - - -
97B GLU* 2.8 26.1 - - + +
124B VAL 3.6 10.8 - - - -
125B SER* 3.9 3.8 - - - -
126B ASP* 3.4 35.7 - - - -
134B ARG* 3.5 32.5 - - - +
304B ILE* 3.2 31.3 + - + +
306B THR 3.7 0.2 - - - -
307B CYS* 1.3 75.3 - - - +
309B ASN* 1.3 63.2 + - - +
310B GLY* 3.1 26.9 - - - -
311B ALA* 3.0 23.8 - - - -
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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