Contacts of the strand formed by residues 338 - 346 (chain A) in PDB entry 3H40
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 LYS 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A VAL* 5.0 0.2 - - - -
336A GLY 3.9 1.8 + - - +
337A ARG* 1.3 75.5 - - - +
339A PRO* 1.3 68.3 - - + +
340A HIS* 3.5 11.5 - - - +
369A ILE* 3.7 28.0 - - + +
413A LEU* 3.8 4.0 - - - -
414A LYS 3.0 31.7 + - - +
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Residues in contact with PRO 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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332A VAL* 3.2 24.7 - - + -
338A LYS* 1.3 87.5 - - + +
340A HIS* 1.3 64.7 + - - +
341A THR 3.4 5.2 - - - +
364A ILE* 3.8 10.7 - - + +
369A ILE* 4.1 12.4 - - + +
410A PHE* 3.4 41.3 - - + -
411A CYS 3.7 15.5 - - - +
412A ASN 3.9 0.9 - - - +
413A LEU* 3.7 17.3 - - + -
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Residues in contact with HIS 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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338A LYS* 3.5 21.0 + - + +
339A PRO* 1.3 80.5 - - - +
341A THR* 1.3 66.1 + - - +
363A PRO* 3.8 6.8 - - - +
364A ILE* 3.5 22.7 + - - +
369A ILE* 3.6 27.0 - - + +
412A ASN* 3.0 25.5 + - - +
414A LYS* 3.7 33.1 + - + +
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Residues in contact with THR 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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339A PRO* 3.4 2.3 - - - +
340A HIS* 1.3 86.3 + - - +
342A VAL* 1.3 72.3 + - - +
361A GLN* 3.8 28.0 + - + +
362A CYS 3.8 12.6 - - - +
363A PRO* 4.9 2.1 - - + +
364A ILE* 3.6 11.4 - - - +
410A PHE* 3.7 3.5 - - - -
411A CYS* 3.1 38.0 + - - +
412A ASN* 3.1 30.9 + - - +
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Residues in contact with VAL 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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341A THR* 1.3 80.0 - - - +
343A ARG* 1.3 73.5 + - - +
361A GLN* 3.7 0.5 - - - -
362A CYS* 3.1 46.2 + - - +
364A ILE* 3.7 18.3 - - + +
383A MET* 4.6 6.7 - - - -
386A ILE* 6.1 1.1 - - + -
387A LEU* 3.4 33.7 - - + -
390A LEU* 4.0 5.2 - - + -
408A VAL* 4.0 16.6 - - + -
409A CYS 3.5 6.5 - - - +
410A PHE* 4.3 15.3 - - + -
411A CYS* 5.4 0.4 - - - -
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Residues in contact with ARG 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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342A VAL* 1.3 81.5 - - - +
344A LEU* 1.3 79.2 + - - +
345A ILE* 4.0 17.9 - - + +
359A SER* 3.6 33.3 + - - -
360A ARG 3.8 14.1 - - - +
361A GLN* 3.2 31.9 + - + +
407A SER 4.5 0.2 - - - -
408A VAL* 3.4 8.8 - - - +
409A CYS* 3.0 43.9 + - + +
411A CYS* 4.2 19.0 - - - -
867P A 5.6 4.2 + - - -
868P G 5.3 11.3 + - - -
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Residues in contact with LEU 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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321A ILE* 4.4 20.2 - - + -
343A ARG* 1.3 85.1 - - - +
345A ILE* 1.3 65.2 + - - +
346A ILE* 5.7 2.2 - - + -
359A SER* 2.8 24.9 - - - -
360A ARG 3.2 7.5 + - - +
387A LEU* 3.2 64.6 - - + +
390A LEU* 3.4 28.3 - - + -
391A PHE* 4.4 7.4 - - - +
394A MET* 4.0 12.4 - - - +
407A SER 3.5 6.1 - - - +
408A VAL* 4.9 4.3 - - + -
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Residues in contact with ILE 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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343A ARG* 4.0 22.4 - - + +
344A LEU* 1.3 76.7 - - - +
346A ILE* 1.3 76.0 + - - +
357A ARG* 4.0 36.3 - - + +
358A GLU 3.0 11.9 - - - +
359A SER* 3.5 13.5 - - - +
405A LEU 5.2 0.4 - - - -
406A LEU* 3.6 3.5 - - - +
407A SER* 3.1 46.5 + - - +
409A CYS* 5.3 8.5 - - + -
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Residues in contact with ILE 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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344A LEU* 5.1 2.2 - - + -
345A ILE* 1.3 86.0 - - - +
347A ARG* 1.3 68.2 + - - +
348A ARG* 4.1 17.7 - - + +
356A GLY 4.0 0.2 - - - +
357A ARG* 3.5 12.1 - - - +
358A GLU* 2.9 40.4 + - + +
391A PHE* 5.9 7.6 - - + -
394A MET* 3.8 46.4 - - + +
405A LEU* 3.2 11.0 - - - +
406A LEU* 3.4 20.9 - - + -
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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