Contacts of the helix formed by residues 304 - 311 (chain A) in PDB entry 1ATT
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 MET 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A ALA* 5.5 9.2 - - + -
296A VAL* 6.5 0.9 - - - -
299A GLU* 4.0 23.8 - - + +
300A LEU* 4.8 8.5 - - + -
301A THR* 2.8 34.3 + - - +
303A ASP* 1.3 77.7 - - - +
305A LEU* 1.4 49.1 + - - +
306A GLN* 2.8 34.1 + - - +
307A GLU* 2.9 55.6 + - - +
308A TRP* 3.1 12.2 - - + -
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Residues in contact with LEU 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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54A LYS* 6.0 6.1 - - + +
302A PRO* 3.3 17.2 + - + +
303A ASP* 3.4 3.6 - - - -
304A MET 1.4 72.4 - - - +
306A GLN* 1.4 54.2 + - - +
307A GLU 3.3 0.4 - - - -
308A TRP* 3.0 19.7 + - + -
309A LEU* 2.8 67.3 + - + +
414A ARG* 3.8 15.9 - - - +
419A ASN* 3.6 25.6 - - + +
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Residues in contact with GLN 306 (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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264A VAL* 6.3 0.2 - - + -
303A ASP 5.0 3.8 - - - +
304A MET* 2.9 28.0 - - + +
305A LEU* 1.4 72.8 - - - +
307A GLU* 1.3 62.6 + - - +
309A LEU* 3.4 14.1 - - + +
310A ASP* 2.6 42.9 + - + +
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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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264A VAL* 3.3 34.8 - - + +
265A ALA* 4.7 8.0 - - - +
268A THR* 4.3 13.7 - - - +
270A VAL* 3.8 21.5 - - + -
285A ILE* 5.1 9.9 - - + +
296A VAL* 5.2 5.5 - - - +
300A LEU* 5.6 3.1 - - - +
304A MET* 2.9 47.7 + - - +
306A GLN* 1.3 77.5 - - - +
308A TRP* 1.3 62.0 + - + +
310A ASP* 2.7 22.2 - - - +
311A GLU* 2.7 21.9 - - - +
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Residues in contact with TRP 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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61A THR* 6.0 2.5 - - + -
270A VAL* 5.1 2.2 - - + -
272A GLU* 5.0 2.2 - - - +
283A VAL* 3.8 29.9 - - + +
285A ILE* 5.1 7.9 - - + -
300A LEU* 4.7 18.6 - - + -
301A THR 4.5 3.8 - - - -
302A PRO* 4.4 11.4 - - + -
304A MET* 3.1 33.2 - - + -
305A LEU* 3.0 35.8 + - + +
306A GLN 3.3 0.2 - - - -
307A GLU* 1.3 90.4 - - + +
309A LEU* 1.3 60.3 + - - +
310A ASP 2.9 5.0 + - - -
311A GLU* 2.9 30.5 + - - +
312A LEU* 5.0 1.6 - - - +
412A LEU* 3.6 32.0 - - + +
414A ARG* 3.1 47.4 - - - +
421A ILE* 5.0 4.9 - - + -
424A MET* 6.4 0.2 - - + -
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Residues in contact with LEU 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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305A LEU* 2.8 36.3 + - + +
306A GLN* 3.4 29.6 - - + +
308A TRP* 1.3 72.6 - - - +
310A ASP* 1.3 62.9 + - + +
311A GLU 3.3 0.4 + - - -
312A LEU* 3.8 29.2 + - + +
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Residues in contact with ASP 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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262A ARG* 3.1 52.2 + - - +
264A VAL* 4.2 13.2 - - - +
306A GLN* 2.6 29.4 + - + +
307A GLU* 2.7 22.0 - - - +
308A TRP 2.9 0.8 + - - -
309A LEU* 1.3 72.5 - - + +
311A GLU* 1.3 58.7 + - - +
312A LEU* 2.9 12.9 + - - +
313A THR* 3.5 8.5 + - - +
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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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260A ARG* 3.2 25.7 - - + +
261A TYR* 3.3 34.4 + - - +
262A ARG* 3.4 8.5 - - + +
270A VAL* 3.5 26.4 - - - +
272A GLU* 3.8 26.0 - - - +
283A VAL* 5.1 0.9 - - - +
307A GLU 2.7 24.3 - - - +
308A TRP* 2.9 29.7 + - - +
310A ASP* 1.3 78.7 + - - +
312A LEU* 1.3 57.4 + - + +
313A THR* 2.8 18.6 + - - -
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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