Contacts of the strand formed by residues 381 - 385 (chain A) in PDB entry 4NAM
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 THR 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A VAL* 3.5 17.8 - - + +
366A TYR* 4.4 2.3 - - - -
379A PRO 3.9 5.2 + - - -
380A THR* 1.3 77.5 - - - +
382A SER* 1.3 67.6 + - - +
383A LEU 4.1 0.2 + - - -
393A THR* 3.4 3.6 - - - +
394A ILE* 2.7 53.2 + - + +
450A LEU* 3.8 34.5 - - + -
451A ASP 3.2 6.3 - - - +
452A THR* 2.9 28.3 + - - +
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Residues in contact with SER 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A THR* 5.8 0.9 - - - +
381A THR* 1.3 76.5 + - - +
383A LEU* 1.3 59.9 + - - +
384A VAL* 3.8 14.7 - - - +
390A THR* 4.4 13.0 - - - +
392A ALA 3.5 8.4 + - - -
393A THR* 4.7 6.6 + - - +
449A ARG 3.4 2.1 - - - +
450A LEU* 3.4 5.4 - - - -
451A ASP* 2.8 42.8 + - - -
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A MET* 4.3 9.9 - - + -
360A LEU* 4.2 23.8 - - + -
381A THR* 4.1 1.0 + - - +
382A SER* 1.3 70.3 - - - +
384A VAL* 1.3 55.3 + - - +
390A THR* 3.5 3.3 - - - -
391A LEU* 2.8 37.1 + - + -
392A ALA* 2.9 19.8 + - + +
394A ILE* 4.5 5.6 - - + +
421A LEU* 4.9 3.1 - - + -
432A ILE* 4.1 32.8 - - + -
448A LEU* 3.9 31.0 - - + -
449A ARG 3.4 8.3 - - - +
450A LEU* 3.6 26.9 - - + -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A SER* 3.8 21.8 - - - +
383A LEU* 1.3 79.8 - - - +
385A LEU* 1.3 64.4 + - - +
386A GLY 3.9 5.3 + - - +
387A LYS 3.7 8.5 - - - +
388A ASN* 3.8 2.9 - - - -
389A GLN 3.4 24.7 - - - +
390A THR* 4.2 9.0 - - - +
391A LEU* 5.0 0.4 - - - -
448A LEU* 3.6 10.6 - - - +
449A ARG* 2.8 60.9 + - + +
451A ASP* 3.9 18.6 - - - +
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Residues in contact with LEU 385 (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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383A LEU 4.3 0.2 + - - -
384A VAL* 1.3 70.7 - - - +
386A GLY* 1.3 74.3 + - - +
387A LYS 3.5 0.2 + - - -
389A GLN* 2.7 46.7 + - + +
391A LEU* 3.9 23.5 - - + +
434A MET* 5.0 1.3 - - + -
438A GLN* 3.6 42.2 - - + +
441A GLU* 3.9 22.0 - - + +
442A LEU* 4.0 42.6 - - + +
445A THR* 4.5 2.2 - - - +
447A GLN 4.2 4.5 - - - +
448A LEU* 4.2 4.9 - - + -
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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