Contacts of the helix formed by residues 295 - 308 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A LYS* 4.8 7.4 - - - +
288A LEU 3.7 8.5 - - - +
289A LEU* 3.7 16.2 - - + -
293A GLY 3.5 5.6 - - - +
294A PHE* 1.4 102.0 - - + +
296A VAL* 1.3 61.2 + - - +
297A ALA* 3.2 5.8 - - + +
298A LYS* 2.9 61.0 + - + +
299A ASP 3.7 0.2 + - - -
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A MET* 3.7 26.8 - - + +
139A PHE* 4.8 2.0 - - + -
233A ILE* 4.4 6.5 - - + -
263A MET* 3.8 20.6 - - + -
284A ILE* 4.2 3.4 - - + -
288A LEU* 3.0 34.9 + - + +
289A LEU 3.9 2.0 - - - +
290A TYR* 3.8 48.5 - - + +
294A PHE 3.2 0.8 + - - -
295A PRO* 1.3 71.4 - - - +
297A ALA* 1.4 60.5 + - - +
299A ASP* 3.0 14.7 + - - +
300A PHE* 3.2 10.0 + - - +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 4.1 13.3 - - + -
284A ILE* 3.8 41.8 - - + +
285A PRO 4.6 5.4 - - - +
286A LYS* 5.7 2.7 - - - -
288A LEU 4.5 0.8 + - - -
295A PRO* 3.2 6.2 - - + -
296A VAL* 1.4 77.2 - - - +
298A LYS* 1.3 59.7 + - - +
300A PHE* 3.9 1.3 - - - +
301A ASN* 3.0 30.0 + - - +
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A PHE* 3.7 19.9 - - + -
295A PRO* 2.9 43.2 + - + +
297A ALA* 1.3 82.6 - - - +
299A ASP* 1.3 60.9 + - - +
301A ASN* 3.8 7.2 - - + +
302A ARG* 3.3 20.4 + - - +
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Residues in contact with ASP 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A MET* 3.9 16.2 - - + -
290A TYR* 3.5 20.4 + - + -
294A PHE* 3.3 8.8 - - + -
295A PRO 3.7 0.8 + - - -
296A VAL 3.0 9.5 + - - +
298A LYS* 1.3 79.1 - - - +
300A PHE* 1.3 59.8 + - - +
301A ASN 3.2 0.4 - - - -
302A ARG* 3.1 8.1 + - - +
303A ILE* 2.9 30.0 + - - +
26B ARG* 2.8 45.4 + - - +
27B ASN 5.0 0.7 + - - -
30B MET* 3.6 28.1 - - + +
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Residues in contact with PHE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.5 48.0 - + + -
131A ASP* 4.1 19.1 - - - -
134A ARG* 3.8 31.9 - - + -
135A LEU* 3.7 29.2 - - + -
138A MET* 3.3 15.1 - - + -
282A THR* 4.1 14.4 - - + -
284A ILE* 3.6 23.3 - - + -
296A VAL 3.2 5.0 + - - +
297A ALA 3.5 5.4 + - - +
299A ASP* 1.3 74.6 - - - +
301A ASN* 1.3 57.0 + - - +
303A ILE* 3.2 6.1 + - + +
304A ILE* 3.0 50.2 + - + +
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Residues in contact with ASN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 3.8 16.1 + - - +
123A PHE* 3.5 23.8 - - + -
297A ALA 3.0 18.2 + - - +
298A LYS* 3.8 8.4 + - + +
300A PHE* 1.3 78.1 - - - +
302A ARG* 1.3 60.9 + - - +
304A ILE* 3.4 5.5 + - - +
305A CYS* 3.1 43.3 + - - -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LYS 3.3 11.5 + - - +
299A ASP* 3.1 12.7 + - - +
301A ASN* 1.3 81.0 - - - +
303A ILE* 1.3 57.8 + - - +
305A CYS* 4.0 3.2 - - - +
306A THR* 2.6 72.4 + - + +
30B MET* 3.6 21.5 - - + -
33B LEU* 3.7 30.9 - - + +
34B GLN* 3.8 11.5 + - - +
36B GLY* 3.1 30.0 + - - -
37B TYR* 3.5 31.2 - - - +
157B ASP* 3.5 19.6 + - - +
175B TYR* 5.6 0.4 + - - -
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 4.0 35.4 - - + +
137A VAL* 3.6 17.5 - - + -
138A MET* 4.0 17.5 - - + +
299A ASP 2.9 15.4 + - - +
300A PHE* 3.2 11.2 + - + +
302A ARG* 1.3 72.9 - - - +
304A ILE* 1.3 56.4 + - + +
306A THR* 4.6 3.1 - - - -
307A CYS* 2.7 49.4 + - + +
30B MET* 3.8 18.6 - - + -
161B ILE* 3.6 35.0 - - + -
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 3.7 36.5 - - + +
98A GLN* 4.2 7.4 - - + +
123A PHE* 4.8 5.4 - - + -
134A ARG* 3.0 46.4 - - + +
300A PHE* 3.0 42.2 + - + +
301A ASN* 3.7 11.4 - - - +
302A ARG 3.3 0.2 - - - -
303A ILE* 1.3 76.7 - - - +
305A CYS* 1.3 60.7 + - - +
308A PHE* 2.9 41.2 + - + +
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Residues in contact with CYS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 3.9 25.2 - - - +
301A ASN* 3.1 31.7 + - - +
302A ARG* 4.0 6.1 - - - +
303A ILE 3.3 0.2 - - - -
304A ILE* 1.3 79.7 - - - +
306A THR* 1.3 58.1 + - - +
36B GLY 5.9 0.2 - - - +
37B TYR* 3.8 27.6 - - + -
40B PRO* 5.2 11.2 - - + -
129B LYS* 2.8 27.0 + - - -
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ARG* 2.6 51.0 + - - +
303A ILE 4.5 0.7 - - - +
305A CYS* 1.3 79.3 - - - +
307A CYS* 1.3 67.0 + - - +
308A PHE 3.8 0.7 - - - -
37B TYR* 4.2 11.2 - - - -
129B LYS* 3.5 18.9 - - - +
154B ALA* 4.4 10.8 + - - +
157B ASP* 3.8 19.1 - - + +
158B SER* 4.2 7.4 + - - -
161B ILE* 3.8 19.7 - - + +
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Residues in contact with CYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 5.0 5.5 + - + +
137A VAL* 5.2 4.5 - - + -
303A ILE* 2.7 39.3 + - + +
306A THR* 1.3 89.4 - - - +
308A PHE* 1.3 58.2 + - + +
129B LYS* 3.6 11.4 - - - +
130B CYS* 3.7 6.1 - - - +
133B SER* 2.5 38.2 + - - +
158B SER* 4.8 12.3 - - - -
161B ILE* 4.2 21.1 - - - -
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Residues in contact with PHE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 3.5 12.1 - - - +
124A VAL 3.5 21.3 - - - -
125A SER* 3.8 3.6 - - - -
126A ASP* 3.7 34.1 - - + -
134A ARG* 3.2 31.6 - - - +
304A ILE* 2.9 42.9 + - + +
307A CYS* 1.3 77.1 - - + +
309A ASN* 1.3 65.1 + - - +
310A GLY* 3.2 43.1 - - - -
311A ALA* 3.3 4.3 - - - -
126B ASP* 3.8 11.4 - - - -
129B LYS* 3.0 19.2 + - - -
130B CYS* 3.7 12.6 - - - -
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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