Contacts of the helix formed by residues 258 - 267 (chain A) in PDB entry 2AG1
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 GLN 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A TYR* 3.9 30.9 + - - -
256A LEU* 3.9 19.5 - - + +
257A VAL* 1.3 80.6 - - - +
259A ASN* 1.3 64.8 + - + +
261A TYR* 2.8 32.2 + - - +
283A ASN 5.0 1.3 + - - +
291A LEU* 3.4 12.6 - - - +
356A ARG* 3.6 18.1 + - - +
401A SER* 3.0 32.8 + - - +
402A GLU* 4.1 2.1 - - - +
552A GLU* 3.6 33.8 + - - +
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Residues in contact with ASN 259 (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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236A PHE* 3.7 5.4 - - - -
254A GLY 3.2 17.5 + - - +
256A LEU* 2.8 19.4 + - - +
257A VAL 3.2 0.4 - - - -
258A GLN* 1.3 78.3 + - + +
260A LEU* 1.3 56.4 + - - +
261A TYR* 3.1 6.0 + - - -
262A SER* 4.3 8.1 + - - -
263A PHE* 3.1 20.6 - - - -
352A LEU* 5.2 1.6 - - - +
353A ALA* 4.1 23.4 + - - +
356A ARG* 3.7 33.7 - - + +
402A GLU* 5.8 0.4 + - - -
405A SER* 3.3 31.5 + - - -
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Residues in contact with LEU 260 (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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208A VAL* 4.4 18.2 - - + -
210A VAL* 4.7 4.0 - - + -
236A PHE* 3.5 31.8 - - + -
257A VAL* 2.8 35.6 + - + +
259A ASN* 1.3 77.5 + - - +
261A TYR* 1.3 63.6 + - - +
262A SER 3.4 0.4 - - - -
263A PHE* 3.2 42.7 - - + +
264A ALA 4.6 0.2 + - - -
270A PRO* 3.9 18.8 - - + -
273A VAL* 6.4 0.4 - - + -
290A GLN 4.0 4.6 - - - +
291A LEU* 3.6 33.2 - - + +
292A ILE* 4.9 3.1 - - + -
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Residues in contact with TYR 261 (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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258A GLN 2.8 15.9 + - - +
259A ASN 3.1 0.4 - - - -
260A LEU* 1.3 78.3 - - - +
262A SER* 1.3 69.4 + - - +
263A PHE 3.2 4.7 + - - -
264A ALA* 4.1 8.8 + - - +
265A LYS 5.2 0.2 + - - -
290A GLN* 3.6 49.5 + - + +
291A LEU* 3.4 12.9 - - + +
356A ARG* 4.2 13.5 - - - +
552A GLU* 5.6 1.3 - - - +
555A ILE* 3.5 36.9 - - + +
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Residues in contact with SER 262 (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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259A ASN* 4.3 9.7 + - - -
260A LEU 3.4 0.4 - - - -
261A TYR* 1.3 88.1 - - - +
263A PHE* 1.3 64.4 + - - +
264A ALA 3.4 1.1 + - - -
265A LYS* 3.5 10.0 + - - +
266A ALA* 3.2 21.8 + - - +
352A LEU* 4.8 17.4 + - - +
355A GLU* 5.4 2.6 + - - -
356A ARG* 5.6 6.5 + - - +
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Residues in contact with PHE 263 (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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236A PHE* 4.1 10.5 - + - -
259A ASN* 3.1 24.5 - - - -
260A LEU* 3.2 44.4 + - + +
261A TYR 3.1 1.6 - - - -
262A SER* 1.3 75.8 - - - +
264A ALA* 1.3 60.2 + - - +
266A ALA* 3.1 11.1 + - - +
268A ALA* 2.8 53.7 + - + +
269A ALA* 3.7 7.2 - - - +
270A PRO* 4.2 4.7 - - + -
345A TRP* 3.7 20.9 - + - -
349A VAL* 3.9 26.5 - - + -
352A LEU* 3.6 37.5 - - + -
353A ALA* 5.2 1.3 - - + -
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Residues in contact with ALA 264 (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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260A LEU 4.6 0.2 + - - -
261A TYR 4.1 7.2 + - - +
262A SER 3.4 0.4 - - - -
263A PHE* 1.3 76.3 - - - +
265A LYS* 1.3 54.4 + - - +
267A ASP* 2.8 30.8 + - - +
269A ALA* 3.8 22.4 - - + +
289A GLY 5.9 3.1 - - - +
290A GLN* 5.7 4.3 - - - +
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Residues in contact with LYS 265 (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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262A SER* 3.5 11.5 + - - +
263A PHE 3.4 0.2 - - - -
264A ALA* 1.3 78.0 - - - +
266A ALA* 1.3 55.9 + - - +
267A ASP* 3.4 2.3 + - - -
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Residues in contact with ALA 266 (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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262A SER 3.2 15.0 + - - +
263A PHE 3.1 6.4 + - - +
264A ALA 3.0 1.6 + - - -
265A LYS* 1.3 76.9 - - - +
267A ASP* 1.3 70.7 + - - +
268A ALA* 3.2 4.5 + - + +
348A LYS* 4.4 14.7 + - - +
352A LEU* 3.9 30.3 - - + -
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Residues in contact with ASP 267 (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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206A ARG* 4.7 9.2 + - - -
264A ALA 2.8 12.8 + - - +
265A LYS 3.4 1.7 - - - -
266A ALA* 1.3 80.7 - - - +
268A ALA* 1.3 56.6 + - - +
269A ALA* 3.6 3.5 + - - -
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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