Contacts of the helix formed by residues 298 - 309 (chain A) in PDB entry 2QDC
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 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A HIS 4.4 3.4 + - - -
61A LEU* 4.3 5.1 - - + +
66A LEU* 4.2 12.3 - - + -
296A VAL* 3.7 15.8 + - + -
297A ASP* 1.3 70.1 + - - +
299A LEU* 1.3 67.1 + - - +
301A ILE* 3.2 9.9 + - + +
302A VAL* 3.1 22.5 + - - +
319A TYR* 3.9 11.7 - - + -
322A LEU* 4.1 20.6 - - + -
323A HIS* 3.5 58.3 - - + +
326A LEU* 3.7 30.7 - - + -
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Residues in contact with LEU 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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53A PHE* 4.7 8.3 - - + -
57A ALA* 4.3 9.0 - - + -
58A GLY 3.8 30.5 - - - +
59A HIS* 4.0 9.2 + - + +
79A GLU* 3.8 28.9 + - + +
83A ILE* 3.7 33.0 - - + -
297A ASP* 3.4 6.4 + - - +
298A ILE* 1.3 79.6 - - - +
300A GLY* 1.3 62.3 + - - +
302A VAL* 3.4 1.4 + - - +
303A CYS* 3.0 34.6 + - - -
319A TYR* 3.4 18.6 + - - +
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Residues in contact with GLY 300 (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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57A ALA 3.9 17.0 - - - -
58A GLY* 4.3 0.2 - - - -
297A ASP* 2.9 24.5 + - - -
299A LEU* 1.3 75.5 - - - +
301A ILE* 1.3 63.4 + - - +
303A CYS* 3.3 4.2 + - - +
304A GLN* 2.9 33.8 + - - +
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Residues in contact with ILE 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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282A ALA* 3.7 36.6 - - + +
285A ILE* 3.9 16.3 - - + +
286A GLY* 3.6 33.4 - - - +
289A GLN* 3.4 26.9 - - - +
296A VAL* 3.7 11.4 - - + -
297A ASP 3.0 19.8 + - - +
298A ILE* 3.2 11.6 + - + +
300A GLY* 1.3 75.9 - - - +
302A VAL* 1.3 56.8 + - + +
304A GLN* 3.3 7.7 + - - +
305A LEU* 3.0 32.6 + - + +
326A LEU* 5.4 0.7 - - + -
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Residues in contact with VAL 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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80A PHE* 5.0 0.4 - - + -
83A ILE* 3.9 20.0 - - + -
282A ALA* 4.8 4.0 - - + -
298A ILE* 3.1 16.6 + - + +
299A LEU 3.9 3.4 - - - +
301A ILE* 1.3 72.2 - - + +
303A CYS* 1.3 65.5 + - - +
305A LEU* 3.2 8.0 + - + +
306A ARG* 3.0 40.5 + - + +
312A MET 4.0 19.5 - - - +
313A ILE* 3.7 28.5 - - + -
319A TYR* 3.7 23.3 - - + -
322A LEU* 4.0 6.7 - - + -
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Residues in contact with CYS 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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53A PHE* 3.8 28.5 - - - -
54A LEU* 3.3 39.4 - - - +
57A ALA* 3.8 17.0 - - - +
83A ILE* 4.2 4.9 - - - -
299A LEU* 3.0 28.8 + - - +
300A GLY* 3.6 7.4 - - - +
302A VAL* 1.3 76.3 - - - +
304A GLN* 1.3 61.6 + - - +
306A ARG* 3.3 4.6 + - - +
307A LEU* 3.1 24.9 + - - +
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Residues in contact with GLN 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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54A LEU 3.6 20.6 + - - -
55A ARG* 4.4 11.3 + - - +
57A ALA 5.8 1.0 + - - -
135A ARG* 2.9 57.8 + - + +
300A GLY* 2.9 24.9 + - - +
301A ILE* 3.7 5.8 - - - +
303A CYS* 1.3 72.5 - - - +
305A LEU* 1.3 65.8 + - + +
307A LEU* 3.3 13.3 + - - +
308A ASP* 3.3 16.6 + - - +
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Residues in contact with LEU 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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134A ILE* 3.5 30.2 - - + +
135A ARG 4.7 1.3 - - - +
278A GLY* 3.6 32.1 - - - +
281A ILE* 3.7 15.5 - - + -
282A ALA* 3.7 21.8 - - + +
285A ILE* 4.3 8.1 - - + -
301A ILE* 3.0 21.1 + - + +
302A VAL* 3.2 12.5 + - - +
304A GLN* 1.3 77.5 - - + +
306A ARG* 1.3 56.0 + - - +
308A ASP* 3.0 8.5 + - - +
309A ARG 2.9 27.7 + - - +
312A MET* 3.7 21.3 - - + +
313A ILE* 4.8 3.6 - - + -
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Residues in contact with ARG 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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54A LEU* 4.0 13.5 - - + -
80A PHE* 3.4 24.7 + - - -
83A ILE* 3.1 32.3 + - + +
84A PRO 2.9 26.9 + - - +
85A SER* 3.4 20.0 - - - +
86A ASN* 2.8 23.4 + - - +
302A VAL* 3.0 24.3 + - - +
303A CYS 3.3 7.4 + - - +
305A LEU* 1.3 71.7 - - - +
307A LEU* 1.3 63.3 + - - +
308A ASP 3.5 0.2 + - - -
309A ARG 3.5 18.1 - - - -
311A GLY* 3.7 12.4 + - - +
312A MET 2.8 22.5 + - - +
313A ILE 2.8 26.5 + - - -
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Residues in contact with LEU 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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51A LEU* 3.8 28.9 - - + -
54A LEU* 3.8 28.9 - - + +
55A ARG* 4.0 33.2 - - + +
86A ASN* 3.6 10.2 + - - +
110A ASN* 4.6 5.9 + - - +
112A GLN* 5.6 2.8 - - - +
113A SER* 4.6 3.6 + - - -
135A ARG* 3.8 7.9 - - - +
303A CYS 3.1 18.3 + - - +
304A GLN* 3.5 30.3 - - - +
305A LEU 3.3 0.4 - - - -
306A ARG* 1.3 76.9 - - - +
308A ASP* 1.3 62.9 + - - +
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Residues in contact with ASP 308 (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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110A ASN* 4.4 1.6 - - - +
113A SER* 2.5 30.7 + - - -
132A ASN* 3.4 9.4 + - - +
133A TYR 3.7 5.6 - - - +
134A ILE* 3.5 25.7 - - + +
135A ARG* 2.9 60.9 + - - +
304A GLN* 3.3 14.1 + - - +
305A LEU* 3.0 8.0 + - - +
307A LEU* 1.3 80.5 - - - +
309A ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 309 (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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107A ILE* 4.1 8.8 - - - +
108A LEU 4.6 4.0 + - - +
109A PRO* 4.0 5.9 - - - +
110A ASN* 3.5 6.3 - - - +
130A ASN* 2.9 32.3 + - - -
131A ALA* 3.9 10.5 - - - +
132A ASN* 2.8 34.4 + - - +
134A ILE* 3.8 11.9 - - + -
146A ALA* 3.8 26.1 + - - -
148A GLN 4.1 6.9 - - - +
272A ALA 3.2 24.9 + - - -
273A GLY* 3.0 26.2 + - - -
274A ILE* 3.4 7.5 - - + +
305A LEU 2.9 9.8 + - - +
306A ARG* 3.5 6.1 - - - -
307A LEU 3.6 0.8 - - - -
308A ASP* 1.3 79.8 - - - +
310A GLY* 1.3 77.3 + - - +
311A GLY 3.4 0.7 + - - -
312A MET* 3.0 24.7 - - + +
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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