Contacts of the helix formed by residues 310 - 317 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ALA* 2.5 38.0 + - - +
306B GLU 3.8 11.7 + - - +
307B ARG* 3.1 14.9 + - - +
308B LEU 3.4 0.6 - - - -
309B THR* 1.3 76.2 - - - +
311B GLU* 1.3 61.7 + - - +
312B LYS* 3.2 19.6 + - - +
313B LEU* 3.3 25.0 + - + +
314B LEU* 3.0 23.9 + - - +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B THR 3.4 6.1 + - - -
310B ASN* 1.3 72.5 + - - +
312B LYS* 1.3 73.5 + - + +
314B LEU* 3.5 9.8 - - - +
315B LYS* 2.9 43.3 + - + +
359B LYS* 3.0 39.2 - - + +
361B PHE 3.9 3.1 - - - +
362B LYS* 5.3 0.5 - - - -
363B LEU* 3.1 36.2 + - + +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LYS* 4.7 3.4 - - - +
154A ASP* 2.9 33.9 + - - +
157A ASN* 4.2 25.7 - - + +
158A THR* 4.1 20.5 - - - +
191A ALA* 4.0 13.0 - - + -
310B ASN* 3.2 10.8 + - - +
311B GLU* 1.3 93.6 + - + +
313B LEU* 1.3 53.0 + - - +
315B LYS* 3.1 37.2 - - - +
316B LYS* 2.8 32.6 + - - +
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ASN 4.5 9.6 - - - +
159A LYS 6.0 0.4 - - - +
191A ALA* 4.0 23.6 - - + +
192A ASN* 4.6 17.3 - - + +
195A LEU* 5.5 0.9 - - + -
278B LEU* 3.6 15.4 - - + +
307B ARG* 5.0 20.9 - - + +
310B ASN* 3.2 34.8 + - + +
312B LYS* 1.3 72.4 - - - +
314B LEU* 1.3 57.6 + - - +
315B LYS 3.0 1.6 - - - -
316B LYS* 3.5 16.3 - - + +
317B ALA* 2.6 37.9 + - - +
15F A 4.6 3.3 + - - +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B LEU* 3.8 12.8 - - + +
307B ARG 4.6 0.7 - - - +
308B LEU* 3.1 38.1 - - + +
309B THR* 4.5 0.2 - - - -
310B ASN 3.0 22.1 + - - +
311B GLU* 3.5 6.5 - - - +
313B LEU* 1.3 76.3 - - - +
315B LYS* 1.3 57.8 + - - +
317B ALA 3.5 0.2 + - - -
318B ARG 2.9 7.3 + - - -
319B ILE* 2.9 60.2 + - + +
324B ILE* 4.9 2.2 - - + -
356B ALA* 4.0 15.3 - - + +
359B LYS* 3.9 30.5 - - + -
360B SER* 4.6 10.1 - - - +
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Residues in contact with LYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LYS* 5.0 6.9 - - - +
154A ASP* 4.8 3.0 + - - -
158A THR* 6.0 1.3 - - + -
83B GLU 6.0 1.3 - - - +
311B GLU* 2.9 28.0 + - + +
312B LYS* 3.1 37.5 - - - +
314B LEU* 1.3 75.7 - - - +
316B LYS* 1.3 64.7 + - - +
318B ARG* 3.1 19.0 + - - +
359B LYS 5.4 2.5 - - - +
360B SER* 5.7 7.6 - - - +
361B PHE 5.7 0.7 - - - -
362B LYS* 4.0 37.5 - - - +
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 3.0 43.5 - - - +
159A LYS 3.8 7.3 + - - +
160A ASP* 3.0 26.3 + - - +
312B LYS 2.8 19.7 + - - +
313B LEU* 3.0 19.2 + - + +
315B LYS* 1.3 74.0 - - - +
317B ALA* 1.3 59.5 + - - +
318B ARG* 3.2 11.2 + - - +
14F A 3.5 9.9 - - - -
15F A 2.7 69.0 + - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B LEU* 3.7 28.7 - - + +
279B THR* 4.6 1.8 + - - +
313B LEU 2.6 20.1 + - - +
316B LYS* 1.3 72.4 - - - +
318B ARG* 1.3 70.4 + - - +
319B ILE* 3.5 11.6 + - + +
13F C 3.4 21.4 - - + +
14F A 4.9 1.1 - - - +
15F A 3.5 23.6 - - - +
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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