Contacts of the strand formed by residues 339 - 343 (chain B) 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 VAL 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313B PHE* 3.8 35.7 - - + -
314B GLU 4.0 6.3 - - - +
317B MET* 3.5 13.9 - - + +
319B ALA* 4.0 8.7 - - + -
333B ILE* 3.8 34.8 - - + +
337B ILE* 3.9 8.2 + - + -
338B THR* 1.3 81.5 - - - +
340B HIS* 1.3 66.0 + - - +
341B LEU* 3.8 28.8 + - + +
374B LEU* 5.5 6.9 - - - +
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Residues in contact with HIS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ALA* 6.0 2.0 - - + -
263A GLN* 3.5 25.6 + - - +
316B GLY* 4.0 17.0 - - - -
317B MET 2.7 17.5 + - - +
318B TYR* 3.4 44.4 + + + +
319B ALA 2.9 24.8 + - - +
338B THR* 3.5 28.1 - - + +
339B VAL* 1.3 74.9 + - - +
341B LEU* 1.3 63.4 + - - +
342B GLN 3.8 0.3 + - - -
348B LEU* 4.2 8.8 - - + +
349B GLY* 5.3 6.3 - - - +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B PHE* 5.0 0.4 - - + -
319B ALA* 3.4 14.4 - - + +
321B LEU* 3.7 33.4 - - + +
327B LEU* 5.0 9.2 - - + -
330B SER* 4.2 17.5 - - - +
333B ILE* 5.2 2.7 - - + -
339B VAL* 3.8 30.2 + - + +
340B HIS* 1.3 71.0 - - - +
342B GLN* 1.3 59.4 + - - +
348B LEU* 3.7 1.0 - - - -
349B GLY* 2.8 33.4 + - - +
350B LEU* 3.1 40.0 + - + +
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Residues in contact with GLN 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ILE* 5.2 1.3 - - + -
318B TYR* 5.9 0.9 - - + -
319B ALA 2.9 16.5 + - - +
320B ASN* 2.8 49.4 + - + +
321B LEU 4.6 1.9 + - - -
340B HIS 3.8 1.1 + - - +
341B LEU* 1.3 74.3 - - - +
343B SER* 1.3 73.6 + - - +
344B GLU 3.8 0.3 + - - -
347B VAL 3.4 9.9 - - - +
348B LEU* 4.1 14.1 - - + -
350B LEU* 4.8 3.9 - - - +
380B PHE* 4.1 4.0 - - + -
385B SER* 3.2 36.4 + - - -
388B MET* 4.0 26.3 - - - -
389B ILE* 3.8 14.0 - - - +
394B VAL* 4.6 12.3 - - + -
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Residues in contact with SER 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B ASN* 4.2 1.6 - - - +
341B LEU 4.3 0.2 + - - -
342B GLN* 1.3 86.8 + - - +
344B GLU* 1.3 59.8 + - - +
345B ASN* 2.3 30.0 + - - -
346B GLY 3.1 16.1 + - - -
347B VAL* 2.8 27.3 + - - +
350B LEU* 3.7 24.0 - - - -
364B ILE 4.2 0.2 + - - -
365B ASN* 3.8 3.7 - - - -
366B ALA* 3.6 16.1 + - - -
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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