Contacts of the helix formed by residues 310 - 317 (chain A) in PDB entry 2I91
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 ASN 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A GLU 3.8 12.3 + - - +
307A ARG 3.1 14.1 + - - +
308A LEU 3.4 0.4 - - - -
309A THR* 1.3 76.8 - - - +
311A GLU* 1.3 62.5 + - - +
312A LYS* 3.2 19.1 + - - +
313A LEU* 3.3 25.5 + - + +
314A LEU* 3.1 23.1 + - - +
191B ALA* 2.4 37.5 + - - +
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Residues in contact with GLU 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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309A THR 3.4 6.7 + - - -
310A ASN* 1.3 72.9 + - - +
312A LYS* 1.3 72.9 + - + +
314A LEU* 3.4 9.6 + - - +
315A LYS* 2.9 45.0 + - + +
359A LYS* 3.0 40.1 - - + +
361A PHE 4.0 2.9 - - - +
362A LYS* 5.3 0.7 - - - -
363A LEU* 3.1 36.7 + - - +
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Residues in contact with LYS 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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310A ASN* 3.2 10.9 + - - +
311A GLU* 1.3 93.3 + - + +
313A LEU* 1.3 53.7 + - - +
315A LYS* 3.1 37.2 - - - +
316A LYS* 2.7 32.2 + - - +
150B LYS* 4.7 3.2 - - - +
154B ASP* 2.8 33.9 + - - +
157B ASN* 4.1 24.0 - - + +
158B THR* 4.0 21.9 - - - +
191B ALA* 4.0 14.4 - - + -
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Residues in contact with LEU 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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278A LEU* 3.5 15.8 - - + +
307A ARG* 5.0 21.3 - - + +
310A ASN* 3.3 35.0 + - + +
312A LYS* 1.3 72.4 - - - +
314A LEU* 1.3 56.8 + - - +
315A LYS 3.0 1.3 - - - -
316A LYS* 3.5 15.8 - - + +
317A ALA* 2.6 38.1 + - - +
157B ASN 4.4 10.1 - - - +
159B LYS 5.9 0.9 - - - +
191B ALA* 4.0 21.5 - - + +
192B ASN* 4.6 20.0 - - + +
195B LEU* 5.5 0.7 - - + -
15D A 5.3 1.5 + - - +
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Residues in contact with LEU 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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278A LEU* 3.8 12.7 - - + +
307A ARG 4.6 0.4 - - - +
308A LEU* 3.1 37.7 - - + +
309A THR* 4.5 0.4 - - - -
310A ASN 3.1 21.6 + - - +
311A GLU* 3.5 6.7 - - - +
313A LEU* 1.3 75.9 - - - +
315A LYS* 1.3 57.4 - - + +
317A ALA 3.5 0.2 + - - -
318A ARG 2.9 7.1 + - - -
319A ILE* 2.8 60.5 + - + +
324A ILE* 4.9 2.0 - - + -
356A ALA* 4.0 16.4 - - + +
359A LYS* 3.9 30.3 - - + +
360A SER* 4.5 10.5 - - - +
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Residues in contact with LYS 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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83A GLU 5.9 2.0 - - - +
311A GLU* 2.9 29.3 + - + +
312A LYS* 3.1 37.1 - - - +
314A LEU* 1.3 75.7 - - - +
316A LYS* 1.3 64.3 + - - +
318A ARG* 3.1 20.5 + - - +
359A LYS 5.4 2.2 - - - +
360A SER* 5.7 7.8 - - - +
361A PHE 5.7 0.7 - - - -
362A LYS* 4.0 36.8 - - - +
150B LYS* 5.0 6.7 - - - +
154B ASP* 4.8 3.0 + - - -
158B THR* 5.9 1.3 - - + -
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Residues in contact with LYS 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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312A LYS 2.7 19.3 + - - +
313A LEU* 3.0 19.9 + - + +
315A LYS* 1.3 73.7 - - - +
317A ALA* 1.3 57.9 + - - +
318A ARG* 3.1 12.6 + - - +
158B THR* 3.0 41.3 - - - +
159B LYS 3.9 7.1 + - - +
160B ASP* 2.8 29.5 + - - +
13D C 5.8 0.2 - - - +
14D A 3.9 8.7 - - - -
15D A 2.3 85.6 + - - +
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Residues in contact with ALA 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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278A LEU* 3.7 26.0 - - + -
279A THR* 4.6 1.5 + - - +
313A LEU 2.6 19.5 + - - +
316A LYS* 1.3 70.3 - - - +
318A ARG* 1.3 70.9 + - - +
319A ILE* 3.4 11.3 + - + +
13D C 3.5 20.4 - - - +
15D A 3.0 33.3 + - - +
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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