Contacts of the helix formed by residues 302 - 309 (chain A) in PDB entry 2NL9
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 LYS 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A PHE* 3.8 42.5 + - + +
257A GLY* 5.7 2.2 - - - -
258A VAL 4.9 0.4 + - - -
259A THR* 2.9 41.1 + - + +
264A ILE* 5.4 2.2 - - + -
297A VAL 4.7 0.4 - - - +
298A LEU* 3.0 25.5 + - + +
301A THR* 1.3 96.7 + - - +
303A ARG* 1.3 66.3 + - - +
304A ASP 3.4 1.8 - - - -
305A TRP* 3.0 25.6 + - + -
306A LEU* 2.8 24.3 + - + +
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Residues in contact with ARG 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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172A ASP* 2.7 43.4 + - - -
174A LEU* 3.8 14.5 - - - +
175A TYR* 4.8 0.4 - - - +
299A VAL* 3.0 41.4 + - - +
300A ARG* 3.8 12.0 + - - +
301A THR 3.6 2.2 - - - -
302A LYS* 1.3 77.3 - - - +
304A ASP* 1.3 73.1 + - - +
306A LEU* 3.1 6.4 + - - +
307A VAL* 2.8 44.1 + - + +
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Residues in contact with ASP 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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302A LYS 3.4 0.4 - - - -
303A ARG* 1.3 92.1 - - - +
305A TRP* 1.3 57.2 + - - +
307A VAL* 3.9 8.3 - - - +
308A LYS* 2.9 33.8 + - - +
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Residues in contact with TRP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A THR* 3.6 44.1 + - + -
260A ASN* 4.0 6.1 - - - -
261A TRP* 3.6 33.4 - + - -
264A ILE* 3.5 28.9 - - + -
302A LYS* 3.0 20.8 + - + +
304A ASP* 1.3 79.3 - - - +
306A LEU* 1.3 73.4 + - + +
308A LYS* 3.8 8.0 + - - +
309A GLN* 3.0 51.8 + - - +
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Residues in contact with LEU 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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174A LEU* 3.9 22.7 - - + -
178A SER* 5.4 0.9 - - - +
261A TRP* 3.5 37.7 - - + -
264A ILE* 5.2 2.5 - - + -
298A LEU* 3.6 29.6 - - + +
299A VAL* 3.9 19.3 - - + -
302A LYS* 2.8 15.7 + - + +
303A ARG* 3.5 5.4 - - - +
305A TRP* 1.3 89.3 - - + +
307A VAL* 1.3 65.1 + - - +
309A GLN* 3.0 10.8 + - - +
311A GLY* 2.8 33.1 + - - -
312A TRP* 5.9 4.5 - - + +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.0 19.1 - - + -
303A ARG* 2.8 34.0 + - + +
304A ASP* 3.9 9.0 - - - +
306A LEU* 1.3 75.7 - - - +
308A LYS* 1.3 65.7 + - - +
310A ARG* 2.9 17.5 + - - +
311A GLY 4.5 2.5 - - - +
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Residues in contact with LYS 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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304A ASP 2.9 17.3 + - - +
305A TRP* 4.2 5.8 - - - +
306A LEU 3.2 0.4 - - - -
307A VAL* 1.3 79.0 - - - +
309A GLN* 1.3 58.3 + - + +
310A ARG* 3.4 6.1 + - - +
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Residues in contact with GLN 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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261A TRP* 2.8 29.6 + - - -
305A TRP* 3.0 56.1 + - - +
306A LEU* 3.0 11.6 + - - +
308A LYS* 1.3 79.7 - - - +
310A ARG* 1.3 75.6 + - - +
311A GLY 3.8 8.5 - - - +
313A ASP* 3.8 4.3 - - - +
314A GLY* 3.3 24.3 + - - -
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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