Contacts of the helix formed by residues 304 - 312 (chain A) in PDB entry 1NH1
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 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TYR* 3.7 3.1 + - - -
164A GLN* 5.4 0.2 - - - -
165A THR 5.0 5.8 - - - -
256A TRP* 3.8 4.3 - - - -
303A SER* 1.3 76.0 + - - +
305A GLU* 1.3 55.6 + - - -
306A GLU 3.3 2.9 - - - -
307A GLU* 2.7 25.1 + - - -
308A PHE* 2.8 31.0 + - - +
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Residues in contact with GLU 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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165A THR 5.2 0.8 + - - -
166A ALA* 6.0 0.2 - - - -
167A TYR* 4.5 10.7 + - - +
229A HIS* 4.8 2.3 - - - -
253A ARG* 2.8 51.6 + - + +
256A TRP* 3.5 37.8 - - + +
257A TRP* 3.0 38.9 + - - -
304A GLY* 1.3 70.1 - - - -
306A GLU* 1.3 66.0 + - + +
308A PHE* 3.3 2.1 + - - +
309A VAL* 2.8 33.9 + - + +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 2.8 40.5 + - - -
304A GLY 3.3 0.6 - - - -
305A GLU* 1.3 86.5 - - + +
307A GLU* 1.3 63.6 + - + +
309A VAL* 3.4 5.5 + - - +
310A GLU* 3.0 24.6 + - - +
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Residues in contact with GLU 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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141A HIS* 5.3 3.7 - - - -
143A ASP* 3.9 18.6 - - - +
162A TYR* 4.3 4.3 + - - -
302A LEU 4.9 0.3 - - - +
303A SER* 3.7 11.4 - - - -
304A GLY* 2.7 35.0 + - - +
306A GLU* 1.3 79.9 - - + +
308A PHE* 1.3 57.6 + - - +
310A GLU* 3.1 15.2 + - - +
311A LYS* 2.8 42.0 + - - +
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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
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252A ALA 3.5 25.4 - - - -
255A HIS* 4.2 7.0 - + + -
256A TRP* 3.5 24.0 - + + -
290A PHE* 5.6 0.4 - + - -
296A SER* 4.0 8.7 - - - -
299A GLU* 3.8 4.9 - - + -
300A ALA* 3.2 37.2 - - + -
303A SER* 3.3 22.1 + - - +
304A GLY 2.8 8.7 + - - +
305A GLU 3.5 8.3 - - - +
307A GLU* 1.3 74.4 - - - +
309A VAL* 1.3 61.3 + - - +
311A LYS* 3.1 7.0 + - + -
312A TYR* 2.7 67.0 + + - +
315A LEU* 4.0 19.1 - - + -
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Residues in contact with VAL 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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248A ILE* 5.7 1.7 - - - +
249A SER* 3.7 37.7 - - - +
252A ALA* 3.8 12.8 - - + -
253A ARG* 3.5 45.3 - - + +
256A TRP* 6.1 0.2 - - + -
305A GLU* 2.8 22.9 + - + +
306A GLU* 3.7 6.3 - - - +
308A PHE* 1.3 76.3 - - + +
310A GLU* 1.3 65.1 + - - +
312A TYR* 3.2 13.3 + - - +
313A ARG* 4.8 2.4 + - - +
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Residues in contact with GLU 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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306A GLU 3.0 12.7 + - - +
307A GLU* 3.4 17.8 - - - +
309A VAL* 1.3 79.6 - - - +
311A LYS* 1.3 60.8 + - + +
312A TYR 3.6 0.3 + - - -
313A ARG* 4.8 7.3 + - - +
314A SER* 5.3 1.4 + - - -
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Residues in contact with LYS 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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137A ARG* 4.9 7.1 - - - +
299A GLU* 4.7 13.4 + - + +
303A SER* 3.9 22.7 - - - -
307A GLU* 2.8 37.4 + - - +
308A PHE* 3.7 9.0 - - + +
310A GLU* 1.3 75.3 - - + +
312A TYR* 1.3 67.9 + - - +
313A ARG 3.4 1.1 - - - -
314A SER* 2.9 28.9 + - - +
315A LEU* 3.1 34.2 - - + +
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Residues in contact with TYR 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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248A ILE* 4.2 20.2 - - + -
251A ILE* 4.0 21.4 - - + +
252A ALA* 3.5 18.4 - - + -
255A HIS* 2.7 37.9 - + - -
276A ALA* 3.9 9.2 - - - +
277A ARG* 5.7 1.4 - - - +
287A LEU* 4.5 11.0 - - + +
290A PHE* 3.8 16.8 - + - -
308A PHE* 2.7 47.5 + + - +
309A VAL 3.2 12.2 + - - +
310A GLU 3.3 0.2 - - - -
311A LYS* 1.3 72.9 - - - +
313A ARG* 1.3 65.4 + - + +
315A LEU* 3.0 24.8 + - + +
316A LEU* 3.7 24.1 + - + +
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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