Contacts of the helix formed by residues 300 - 315 (chain A) in PDB entry 3NUI
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 GLY 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PHE* 3.5 22.3 - - - -
108A SER 4.0 1.8 - - - -
279A ASP* 3.0 23.0 + - - -
299A LEU* 1.3 71.5 - - - +
301A PRO* 1.3 73.7 - - - +
302A GLU 3.4 2.6 + - - -
303A LEU* 3.6 1.8 + - - +
304A SER* 2.7 27.6 + - - -
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Residues in contact with PRO 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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106A PHE* 3.9 18.4 - - + -
107A ASP* 5.0 2.7 - - + +
108A SER* 3.4 36.1 - - - +
109A GLY* 4.8 0.2 - - - -
300A GLY* 1.3 84.4 - - - +
302A GLU* 1.3 59.3 + - - +
304A SER* 3.7 5.2 - - - -
305A LYS* 2.9 31.9 + - - +
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Residues in contact with GLU 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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247A ARG* 5.2 2.6 + - - -
250A ASP* 5.0 2.8 - - - +
279A ASP* 4.1 20.8 - - + +
300A GLY 3.4 0.6 - - - -
301A PRO* 1.3 81.7 - - - +
303A LEU* 1.4 64.8 + - - +
305A LYS* 3.5 7.1 + - + +
306A ARG* 2.6 63.6 + - + +
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Residues in contact with LEU 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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124A MET* 5.1 1.1 - - - -
128A LEU* 4.5 18.6 - - + -
131A LEU* 3.9 25.1 - - + -
252A PRO* 4.6 9.6 - - + -
254A ILE* 4.5 10.5 - - + -
279A ASP* 3.7 42.5 + - + +
280A ALA* 4.1 13.9 - - + -
299A LEU* 4.4 16.8 - - + -
300A GLY 3.6 4.2 + - - +
301A PRO 3.5 0.2 - - - -
302A GLU* 1.4 80.0 - - + +
304A SER* 1.3 57.8 + - - +
306A ARG* 3.4 18.1 + - - +
307A LEU* 2.8 39.4 + - + +
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Residues in contact with SER 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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109A GLY* 3.6 3.3 - - - -
110A ARG* 3.2 34.5 + - - +
299A LEU* 3.0 24.4 + - - +
300A GLY 2.7 23.3 + - - -
301A PRO* 3.7 5.8 - - - -
303A LEU* 1.3 75.9 - - - +
305A LYS* 1.3 52.3 + - - +
307A LEU* 3.3 6.5 + - - +
308A GLU* 2.8 39.5 + - - +
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Residues in contact with LYS 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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301A PRO 2.9 17.7 + - - +
302A GLU* 3.8 7.0 - - + +
304A SER* 1.3 77.2 - - - +
306A ARG* 1.3 60.9 + - + +
308A GLU* 3.4 15.3 + - - +
309A THR* 2.9 47.3 + - + +
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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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131A LEU* 3.5 25.9 - - + +
132A HIS* 4.0 17.8 - - - -
135A GLU* 3.0 39.9 + - - +
140A LYS* 5.8 0.4 - - - +
250A ASP* 4.4 14.0 + - - -
252A PRO* 4.9 7.9 - - - +
302A GLU* 2.6 63.5 + - + +
303A LEU* 3.9 13.5 - - - +
305A LYS* 1.3 78.7 - - + +
307A LEU* 1.3 58.8 + - - +
309A THR* 3.0 9.2 + - - +
310A ALA* 3.0 28.8 + - - +
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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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127A MET* 3.6 43.3 - - + -
130A PHE* 3.8 27.8 - - + -
131A LEU* 4.0 20.0 - - + -
299A LEU* 3.7 31.2 - - + -
303A LEU* 2.8 26.1 + - + +
304A SER* 3.8 4.0 - - - +
306A ARG* 1.3 70.2 - - - +
308A GLU* 1.3 68.3 + - - +
310A ALA* 3.2 0.7 + - - +
311A ILE* 2.9 37.9 + - + +
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Residues in contact with GLU 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 ARG* 4.2 25.4 + - - +
304A SER 2.8 21.6 + - - +
305A LYS* 3.6 14.8 + - - +
307A LEU* 1.3 74.5 - - - +
309A THR* 1.3 59.9 + - - +
311A ILE* 3.4 6.3 + - - +
312A GLU* 2.9 58.2 + - + +
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Residues in contact with THR 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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135A GLU* 5.4 1.4 + - - -
305A LYS* 2.9 43.3 + - + +
306A ARG* 3.0 17.9 + - - +
308A GLU* 1.3 77.0 - - - +
310A ALA* 1.3 59.9 + - - +
312A GLU* 3.1 15.7 + - - +
313A ALA* 2.8 32.0 + - - +
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Residues in contact with ALA 310 (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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130A PHE* 4.5 8.7 - - + -
131A LEU* 3.9 14.4 - - + -
134A ALA* 3.8 27.8 - - + -
135A GLU* 5.5 3.1 - - + -
306A ARG 3.0 17.4 + - - +
307A LEU* 3.7 4.5 - - - +
309A THR* 1.3 77.4 + - - +
311A ILE* 1.3 56.8 + - - +
313A ALA* 3.2 5.8 + - - +
314A ILE* 2.9 36.4 + - - +
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Residues in contact with ILE 311 (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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86A PHE* 4.7 15.3 - - + -
127A MET* 6.5 0.2 - - - -
130A PHE* 4.3 14.6 - - + -
307A LEU* 2.9 27.5 + - + +
308A GLU* 3.8 5.8 - - - +
310A ALA* 1.3 74.2 - - - +
312A GLU* 1.3 67.4 + - + +
314A ILE* 3.8 2.9 - - - +
315A GLU* 3.0 21.5 + - - -
316A GLU 3.7 19.8 + - - +
317A PHE* 4.2 19.7 - - + -
318A PRO* 4.0 29.2 - - + -
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Residues in contact with GLU 312 (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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308A GLU* 2.9 55.1 + - + +
309A THR* 3.1 19.4 + - - +
311A ILE* 1.3 77.7 - - + +
313A ALA* 1.3 62.6 + - - +
315A GLU* 3.1 21.2 + - - +
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Residues in contact with ALA 313 (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 ALA 6.1 0.4 - - - +
309A THR 2.8 21.1 + - - +
310A ALA* 3.2 7.6 + - - +
312A GLU* 1.3 74.0 - - - +
314A ILE* 1.3 65.1 + - + +
315A GLU* 3.3 13.9 + - - +
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Residues in contact with ILE 314 (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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130A PHE* 4.4 14.4 - - + -
134A ALA* 4.3 17.3 - - + +
310A ALA* 2.9 22.5 + - - +
311A ILE* 3.8 3.4 - - - +
313A ALA* 1.3 73.9 - - + +
315A GLU* 1.3 69.9 + - - +
316A GLU* 3.2 48.7 + - + +
317A PHE 5.0 1.8 - - - +
318A PRO* 5.3 0.9 - - + -
163B LYS* 5.8 1.9 + - - -
165B TYR* 3.4 55.7 + - + +
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Residues in contact with GLU 315 (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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311A ILE 3.0 10.3 + - - -
312A GLU* 3.1 17.6 + - - +
313A ALA 3.7 11.1 - - - +
314A ILE* 1.3 76.5 - - - +
316A GLU* 1.3 60.7 + - - +
396B ASN* 6.1 1.2 - - - +
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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