Contacts of the strand formed by residues 401 - 404 (chain A) in PDB entry 1A16
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 ILE 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A CYS* 3.8 2.0 - - - -
256A LEU* 4.1 9.4 - - + -
285A ALA* 4.1 19.1 - - + +
286A GLN* 4.2 21.5 - - + +
289A ILE* 4.3 14.1 - - + -
386A LEU 3.7 1.7 - - - +
387A TYR* 3.4 1.6 - - - -
388A ILE* 2.7 36.7 + - + +
397A GLN 3.6 22.7 - - - +
398A TYR* 3.4 21.5 + - - +
399A ARG 3.3 3.1 - - - +
400A GLY* 1.3 80.0 - - - +
402A GLY* 1.3 59.0 + - - +
403A ILE* 3.8 29.6 - - + -
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Residues in contact with GLY 402 (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 GLY 4.8 3.1 + - - +
239A GLY* 3.6 31.5 - - - +
240A CYS* 3.9 3.4 - - - -
256A LEU* 4.6 5.7 - - - +
258A LEU* 3.8 9.9 + - - +
275A THR* 3.7 12.0 - - - +
386A LEU 3.5 3.6 - - - -
387A TYR* 3.9 5.2 - - - -
400A GLY 3.8 3.4 + - - -
401A ILE* 1.3 73.9 - - - +
403A ILE* 1.3 66.6 + - - +
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Residues in contact with ILE 403 (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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256A LEU* 3.7 27.8 - - + -
258A LEU* 4.0 1.6 - - - -
275A THR* 3.7 12.3 - - + -
286A GLN 3.8 6.5 - - - +
289A ILE* 3.8 14.6 - - + -
290A TYR* 3.5 53.4 - - + +
293A VAL* 3.9 23.8 - - + -
385A GLY* 3.0 3.3 - - - -
386A LEU 2.8 42.0 + - - +
387A TYR* 3.7 3.9 - - - -
401A ILE* 3.8 6.5 - - + -
402A GLY* 1.3 79.3 - - - +
404A ARG* 1.3 66.1 + - - +
405A ILE* 4.3 1.6 - - + -
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Residues in contact with ARG 404 (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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242A LEU* 3.2 30.1 + - - +
258A LEU* 3.7 20.5 - - + +
260A ASP* 3.0 32.7 + - - +
273A THR* 3.3 27.9 + - + +
275A THR* 2.9 22.9 + - - -
293A VAL* 4.4 0.2 - - - -
350A HIS* 4.0 6.5 - - - -
383A GLU* 3.5 25.7 + - + +
384A PRO 3.5 12.8 - - - +
387A TYR* 2.8 50.2 + - - +
403A ILE* 1.3 74.7 - - - +
405A ILE* 1.3 69.8 + - - +
441A PRO* 3.4 22.0 - - - +
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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