Contacts of the helix formed by residues 344 - 353 (chain A) in PDB entry 3A3K
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 ASP 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A THR* 4.5 3.3 - - + +
340A GLY* 3.5 8.8 - - - -
341A THR* 2.9 45.9 + - - +
342A VAL 3.2 0.8 - - - -
343A THR* 1.3 76.6 + - - +
345A GLY* 1.3 64.6 + - - +
346A GLU 3.3 2.2 - - - -
347A ASN* 3.2 16.6 + - + -
348A ILE* 3.0 24.8 + - - +
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Residues in contact with GLY 345 (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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101A ARG 4.3 4.3 + - - -
103A PRO* 3.7 29.1 - - - +
122A LEU* 4.1 12.3 - - - -
343A THR 2.9 12.1 + - - -
344A ASP* 1.3 71.1 - - - +
346A GLU* 1.3 56.4 + - - +
348A ILE* 3.3 4.6 + - - +
349A THR* 2.9 34.5 + - - -
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Residues in contact with GLU 346 (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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101A ARG* 5.1 13.5 - - - +
122A LEU* 3.7 26.0 - - + +
344A ASP 3.3 0.8 - - - -
345A GLY* 1.3 74.9 - - - +
347A ASN* 1.3 58.4 + - - +
349A THR* 3.4 4.2 + - - +
350A GLN* 3.0 34.6 + - - +
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Residues in contact with ASN 347 (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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335A THR* 3.4 11.7 + - + +
344A ASP* 3.2 20.6 + - + +
346A GLU* 1.3 77.9 - - - +
348A ILE* 1.3 63.1 + - - +
350A GLN* 3.1 45.0 + - - +
351A ARG* 3.1 43.1 + - - +
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Residues in contact with ILE 348 (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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103A PRO* 5.2 3.4 - - + -
328A TYR* 3.7 33.0 - - + -
331A ALA* 3.7 11.5 - - + +
332A VAL* 3.8 23.3 - - + -
335A THR* 3.8 24.9 - - + +
341A THR 4.1 3.6 - - - +
342A VAL* 3.1 34.1 - - - +
344A ASP 3.0 21.9 + - - +
345A GLY* 3.8 7.4 - - - +
347A ASN* 1.3 74.2 - - - +
349A THR* 1.3 63.5 + - - +
351A ARG* 3.1 14.4 + - - +
352A MET* 3.4 16.2 + - + +
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Residues in contact with THR 349 (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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103A PRO* 4.1 8.8 - - - +
122A LEU* 3.9 31.2 + - + +
124A THR* 4.0 3.4 - - - +
345A GLY 2.9 19.9 + - - -
346A GLU* 3.9 5.6 - - - +
348A ILE* 1.3 75.8 - - - +
350A GLN* 1.3 62.7 + - - +
352A MET* 3.1 17.0 + - - +
353A TRP* 3.0 64.0 + - + +
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Residues in contact with GLN 350 (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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346A GLU* 3.0 20.2 + - - +
347A ASN* 3.1 51.7 + - - +
348A ILE 3.3 0.2 - - - -
349A THR* 1.3 75.8 - - - +
351A ARG* 1.3 80.9 + - + +
353A TRP* 3.3 23.7 + - - +
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Residues in contact with ARG 351 (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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327A LEU* 5.1 0.2 - - - +
331A ALA* 3.7 18.4 - - + -
334A GLU* 3.7 33.3 + - - +
335A THR* 3.0 29.3 + - - +
338A GLN* 3.5 40.2 + - - +
347A ASN* 3.1 27.8 + - - +
348A ILE 3.1 10.8 + - - +
350A GLN* 1.3 95.9 - - + +
352A MET* 1.3 59.4 + - - +
353A TRP 4.5 0.9 - - - -
355A ARG* 3.1 32.4 + - - +
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Residues in contact with MET 352 (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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103A PRO* 5.2 4.7 - - + -
105A LEU* 4.2 14.4 - - + -
124A THR* 3.7 23.1 - - + +
327A LEU* 4.0 27.1 - - + +
328A TYR* 3.7 37.5 - - + -
331A ALA* 3.7 14.1 - - + -
348A ILE* 3.6 17.0 - - + +
349A THR* 3.1 29.4 + - - +
351A ARG* 1.3 79.0 - - - +
353A TRP* 1.3 69.0 + - + +
355A ARG* 3.3 13.7 - - - +
366A ILE* 3.4 18.4 - - - +
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Residues in contact with TRP 353 (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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117A LYS* 3.9 22.7 - - + -
121A ALA* 5.7 0.2 - - - -
122A LEU* 4.6 7.4 - - + -
123A THR 3.3 24.9 - - - -
124A THR* 2.7 25.9 + - + -
349A THR* 3.0 39.0 + - + +
350A GLN* 3.3 19.0 + - - +
351A ARG 4.5 0.2 - - - -
352A MET* 1.3 79.2 - - + +
354A ASN* 1.3 74.2 + - + +
355A ARG* 3.9 2.8 - - - +
366A ILE* 3.9 7.4 - - + -
367A ASP 4.0 2.9 - - - +
368A ARG 3.6 19.5 - - - +
369A ASN* 3.9 14.6 - - - -
370A GLY* 3.4 24.1 - - - -
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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