Contacts of the helix formed by residues 338 - 347 (chain A) in PDB entry 1A8H
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 GLU 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A VAL* 5.3 2.0 - - + +
311A LEU* 3.8 31.7 - - + +
314A LYS* 3.0 26.6 - - - +
315A TYR* 2.9 29.5 + - + +
337A SER* 1.3 73.3 - - - +
339A GLU* 1.3 67.9 + - - +
341A LEU* 3.5 6.8 + - - +
342A ARG* 3.0 32.5 + - + +
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Residues in contact with GLU 339 (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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293A PRO* 4.3 10.4 - - - +
337A SER* 3.1 30.9 - - - +
338A GLU* 1.3 86.2 + - - +
340A ALA* 1.3 61.3 + - - +
342A ARG* 3.4 7.2 + - - +
343A THR* 3.1 25.8 + - - -
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Residues in contact with ALA 340 (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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323A TYR* 3.5 29.2 - - + +
327A GLU* 4.2 10.0 - - + +
335A PRO 6.0 0.4 - - - +
337A SER* 3.2 17.1 + - - +
339A GLU* 1.3 78.6 - - - +
341A LEU* 1.3 61.5 + - - +
343A THR* 3.5 7.5 + - - +
344A ARG* 3.2 23.9 + - - +
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Residues in contact with LEU 341 (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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311A LEU* 4.4 19.7 - - + +
315A TYR* 3.3 49.6 - - + -
319A ALA* 4.7 4.3 - - + +
320A LEU* 4.1 31.4 - - + +
323A TYR* 3.8 38.3 - - + +
337A SER 3.6 11.0 + - - +
338A GLU* 3.5 7.6 + - - +
339A GLU 3.2 0.6 - - - -
340A ALA* 1.3 78.2 - - - +
342A ARG* 1.3 59.9 + - - +
344A ARG* 3.6 2.5 + - - +
345A TYR* 3.0 25.5 + - + +
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Residues in contact with ARG 342 (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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314A LYS* 4.5 14.3 - - - +
315A TYR* 3.2 40.9 + - + +
338A GLU* 3.0 25.0 + - + +
339A GLU* 3.8 7.4 - - - +
340A ALA 3.3 0.4 - - - -
341A LEU* 1.3 75.7 - - - +
343A THR* 1.3 62.0 + - - +
345A TYR* 3.6 1.9 - - - +
346A GLU* 2.9 48.9 + - - +
500A LYS* 2.7 42.2 + - - +
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Residues in contact with THR 343 (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 GLU* 6.1 0.2 - - - +
339A GLU 3.1 17.3 + - - -
340A ALA* 3.8 6.7 - - - +
341A LEU 3.3 0.2 - - - -
342A ARG* 1.3 76.6 - - - +
344A ARG* 1.3 72.0 + - + +
346A GLU* 3.2 5.6 + - - +
347A ALA* 2.9 30.8 + - + +
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Residues in contact with ARG 344 (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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322A TYR* 3.4 28.3 - - + -
323A TYR* 4.7 9.9 - - + -
326A ARG* 2.7 54.2 - - - +
327A GLU* 2.6 47.4 + - - +
340A ALA 3.2 12.7 + - - +
341A LEU* 4.0 6.3 - - - +
343A THR* 1.3 85.1 - - - +
345A TYR* 1.3 58.4 + - - +
347A ALA* 4.9 0.2 - - - -
348A ASP* 2.9 59.8 + - - +
349A LEU* 3.4 2.6 + - - +
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Residues in contact with TYR 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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315A TYR* 4.0 32.7 + + + -
319A ALA* 3.6 22.0 - - + -
341A LEU* 3.0 20.5 + - + +
342A ARG* 3.6 7.2 - - - +
344A ARG* 1.3 77.9 - - - +
346A GLU* 1.3 69.5 + - - +
349A LEU* 3.4 15.0 + - + +
350A ALA* 2.7 43.0 + - + +
497A PHE* 3.4 25.6 - + + +
498A PRO* 2.6 47.8 + - - +
499A LYS* 5.1 0.4 - - - -
500A LYS* 3.8 26.3 + - + +
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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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342A ARG* 2.9 45.2 + - - +
343A THR* 3.6 6.4 - - - +
345A TYR* 1.3 88.4 - - - +
347A ALA* 1.3 57.5 + - - +
350A ALA* 3.6 9.3 - - + +
351A ASP* 3.1 29.6 + - - +
499A LYS* 6.1 3.4 - - - -
500A LYS* 4.0 16.6 + - - +
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Residues in contact with ALA 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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343A THR* 2.9 20.9 + - + +
344A ARG* 4.9 0.4 - - - -
346A GLU* 1.3 80.0 - - + +
348A ASP* 1.3 72.1 + - - +
351A ASP* 3.3 6.4 - - - +
352A ASP* 2.9 33.7 + - - +
412A LYS* 6.3 0.9 - - - +
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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