Contacts of the helix formed by residues 311 - 319 (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 GLY 311 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 4.4 18.8 - - - -
177A GLN* 5.6 0.9 - - - -
261A TRP* 3.6 17.9 - - - -
306A LEU* 2.8 28.1 + - - -
307A VAL* 4.5 1.2 - - - +
309A GLN* 3.7 4.0 - - - +
310A ARG* 1.3 74.3 - - - +
312A TRP* 1.3 59.9 + - - -
313A ASP 3.0 0.2 - - - -
314A GLY 3.0 18.4 + - - -
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Residues in contact with TRP 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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174A LEU* 4.4 5.3 - - + +
177A GLN* 3.7 24.2 - - - +
178A SER* 2.8 42.1 + - - +
181A ILE* 3.6 30.3 - - + -
182A ILE* 4.2 15.0 - - + -
205A ALA* 5.3 3.6 - - + +
209A ALA* 3.8 19.5 - - + -
213A LEU* 5.2 1.3 - - + -
261A TRP* 4.2 16.2 - + - -
268A ILE* 4.0 25.4 - - + -
298A LEU* 5.3 4.9 - - + -
306A LEU* 5.9 3.6 - - + +
310A ARG 3.1 2.6 + - - -
311A GLY* 1.3 70.7 - - - -
313A ASP* 1.3 60.2 + - - +
314A GLY 3.1 0.2 - - - -
315A PHE* 3.0 51.0 + + + +
316A VAL* 2.8 31.9 + - + +
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Residues in contact with ASP 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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309A GLN 3.8 6.1 - - - +
310A ARG* 2.8 51.4 + - + +
311A GLY 3.0 0.6 + - - -
312A TRP* 1.3 76.9 - - - +
314A GLY* 1.3 63.8 + - - +
316A VAL* 3.7 8.2 - - - +
317A GLU* 2.9 28.0 + - - +
1002A ZN 2.0 35.7 - - - -
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Residues in contact with GLY 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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261A TRP* 3.5 7.8 + - - -
309A GLN* 3.3 31.5 + - - -
311A GLY 3.0 7.8 + - - -
313A ASP* 1.3 81.1 - - - +
315A PHE* 1.3 55.7 + - - +
317A GLU* 4.2 3.4 - - - +
318A PHE* 2.9 31.7 + - - +
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Residues in contact with PHE 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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209A ALA* 3.4 27.4 - - - -
212A THR* 3.4 20.2 - - + -
213A LEU* 3.7 29.8 - - + -
216A VAL* 4.0 3.6 - - + -
261A TRP* 3.5 48.9 - + + -
264A ILE* 5.9 0.2 - - + -
265A VAL* 3.8 17.5 - - + -
268A ILE* 5.8 1.3 - - + -
312A TRP* 3.0 33.4 + + + +
314A GLY* 1.3 74.3 - - - +
316A VAL* 1.3 68.9 + - - +
318A PHE* 3.3 0.6 + - - -
319A PHE* 3.2 54.7 + + - +
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Residues in contact with VAL 316 (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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205A ALA 4.7 2.5 - - - +
208A ARG* 4.0 18.8 - - + +
209A ALA* 3.7 35.7 - - + +
212A THR* 4.2 15.1 + - - +
312A TRP 2.8 23.7 + - - +
313A ASP* 3.7 8.3 - - - +
315A PHE* 1.3 73.9 - - + +
317A GLU* 1.3 77.0 + - - +
319A PHE* 3.7 1.4 - - - +
320A HIS* 3.1 28.5 + - - +
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Residues in contact with GLU 317 (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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313A ASP* 2.9 23.9 + - - +
314A GLY* 4.2 3.4 - - - +
316A VAL* 1.3 84.2 - - - +
318A PHE* 1.3 69.1 + - - +
320A HIS* 3.2 35.1 + - - +
1002A ZN 2.0 38.5 - - - -
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Residues in contact with PHE 318 (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* 3.9 17.7 - + + -
314A GLY 2.9 19.6 + - - +
315A PHE 3.8 3.6 - - - +
317A GLU* 1.3 78.4 - - - +
319A PHE* 1.3 87.9 + + + +
320A HIS 3.7 2.1 + - - +
70B ASN* 3.3 50.9 - - - -
73B TYR* 3.6 31.8 - - + +
74B ALA* 3.8 24.5 - - + -
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Residues in contact with PHE 319 (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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212A THR* 3.6 17.5 - - + -
215A ARG* 2.9 27.4 + - - -
216A VAL* 3.8 17.7 - - + -
261A TRP* 3.8 16.4 - - + -
262A GLY* 4.1 1.8 - - - -
265A VAL* 3.8 19.1 - - + -
315A PHE* 3.2 54.5 + + - -
316A VAL 3.7 2.0 - - - -
318A PHE* 1.3 101.3 - + - +
320A HIS* 1.3 61.8 + - - +
321A VAL* 3.6 3.3 - - - +
69B PHE* 3.7 13.9 - + - -
73B TYR* 3.5 39.8 - + - -
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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