Contacts of the strand formed by residues 396 - 399 (chain A) in PDB entry 3DLX
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 LEU 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A GLU* 3.9 23.8 - - + +
313A PHE* 4.2 13.7 - - + -
317A MET* 3.9 25.1 - - + -
318A TYR 3.1 3.6 + - - -
319A ALA* 3.1 8.6 - - + +
320A ASN 2.9 25.8 + - - -
394A VAL* 3.2 5.6 - - - +
395A ASP* 1.3 80.7 - - - +
397A THR* 1.3 68.5 + - - +
398A MET* 3.9 22.7 - - + +
435A THR* 4.1 0.4 - - - -
436A LYS* 3.4 27.6 - - + +
438A VAL* 3.3 30.7 - - + -
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Residues in contact with THR 397 (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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320A ASN* 3.4 11.8 - - - +
389A ILE* 5.7 0.3 - - - +
394A VAL* 4.4 2.6 - - - +
396A LEU* 1.3 77.9 + - - +
398A MET* 1.3 62.0 + - - +
399A LEU* 3.7 29.2 - - + -
429A LEU* 3.5 49.9 + - + +
435A THR* 3.7 9.7 - - - +
436A LYS 2.8 12.5 + - - +
437A VAL* 3.5 7.5 - - + -
438A VAL 3.0 24.3 + - - -
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Residues in contact with MET 398 (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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309A ALA* 3.7 28.5 - - + +
312A GLU* 3.6 32.1 - - + -
313A PHE* 4.4 7.9 - - + -
320A ASN 3.1 6.7 + - - -
321A LEU* 3.7 26.5 - - + -
322A GLY* 2.7 33.1 + - - -
326A PRO* 3.4 15.2 - - + +
329A ALA* 4.9 2.0 - - - -
396A LEU* 3.9 16.6 - - + -
397A THR* 1.3 71.2 - - - +
399A LEU* 1.3 60.9 + - - +
438A VAL* 3.3 22.0 - - + +
440A THR* 3.7 19.5 - - + -
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Residues in contact with LEU 399 (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 GLY* 4.1 14.4 - - - -
323A ILE 5.5 0.7 - - - +
326A PRO* 3.9 7.4 - - - -
397A THR* 3.7 22.0 - - + -
398A MET* 1.3 79.1 - - - +
400A GLY* 1.3 67.3 + - - +
410A LEU* 4.0 12.1 - - + -
412A ASN* 4.4 11.0 - - - +
426A ALA* 4.5 13.5 - - + +
429A LEU* 4.5 13.5 - - + -
430A VAL* 3.4 32.8 - - + -
437A VAL* 4.6 3.8 - - + -
438A VAL 3.0 9.5 + - - +
439A VAL* 3.2 13.5 - - + -
440A THR 2.9 24.8 + - - -
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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