Contacts of the strand formed by residues 323 - 329 (chain A) in PDB entry 3L5J
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 ARG 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A ILE* 3.3 40.7 - - + +
316A PRO* 4.4 17.0 - - + -
322A TYR* 1.3 77.9 - - - +
324A THR* 1.3 62.9 + - - +
325A VAL* 3.8 4.6 + - + +
368A ASN* 3.7 3.1 - - - -
369A LEU* 2.8 40.9 + - + +
370A THR 3.1 14.0 + - - +
371A ASN* 3.8 20.4 - - - +
372A ASP 2.6 30.3 + - - -
374A TYR* 4.4 2.4 - - - -
394A ILE* 3.7 20.0 - - - +
395A PRO* 3.1 26.1 + - - +
397A CYS* 4.0 13.3 - - - +
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Residues in contact with THR 324 (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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313A LYS 4.0 0.9 - - - +
314A ILE* 3.5 2.3 - - - -
315A ASP* 3.2 42.7 + - - +
316A PRO* 4.6 4.1 - - - +
323A ARG* 1.3 71.9 - - - +
325A VAL* 1.3 65.0 + - - +
326A GLN* 4.2 1.7 + - + +
366A THR* 3.7 29.4 - - + -
367A VAL 3.5 5.2 - - - +
368A ASN* 3.4 18.2 + - - +
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Residues in contact with VAL 325 (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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312A TYR* 4.2 18.4 - - + -
313A LYS 3.6 8.1 - - - +
314A ILE* 4.2 12.8 - - + -
323A ARG* 4.3 12.6 - - + +
324A THR* 1.3 79.3 - - - +
326A GLN* 1.3 63.3 + - - +
327A LEU* 3.8 24.6 + - + -
365A LEU 3.6 1.9 - - - +
366A THR* 3.5 1.9 - - - -
367A VAL* 2.9 37.1 + - + +
369A LEU* 3.6 35.7 - - + -
394A ILE* 4.2 12.1 - - + -
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Residues in contact with GLN 326 (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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312A TYR* 3.7 0.2 - - - -
313A LYS* 2.8 46.2 + - - +
324A THR* 4.2 1.7 + - + -
325A VAL* 1.3 73.1 - - - +
327A LEU* 1.3 62.7 + - - +
328A VAL* 3.5 26.7 + - + +
364A LYS* 4.0 22.2 - - + +
365A LEU 3.3 6.3 - - - +
366A THR* 3.8 21.7 + - + +
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Residues in contact with LEU 327 (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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310A PHE* 4.1 13.5 - - + -
311A TRP 3.9 3.6 - - - +
312A TYR* 3.6 23.3 - - + -
325A VAL* 3.8 15.9 - - + +
326A GLN* 1.3 71.6 - - - +
328A VAL* 1.3 61.7 + - - +
329A TRP* 4.2 13.5 - - + -
346A VAL* 3.8 20.0 - - + -
348A LEU* 3.5 36.3 - - + -
364A LYS* 3.1 3.8 - - - -
365A LEU* 2.7 47.5 + - + +
367A VAL* 5.4 1.8 - - + -
376A ALA* 4.5 0.7 - - + -
392A LEU* 4.6 8.1 - - + -
394A ILE* 4.1 12.1 - - + -
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Residues in contact with VAL 328 (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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310A PHE* 3.5 3.6 - - - -
311A TRP* 2.9 50.4 + - + +
312A TYR* 4.1 4.3 - - - +
313A LYS* 6.2 1.3 - - + -
326A GLN* 3.5 34.3 - - - +
327A LEU* 1.3 81.9 - - - +
329A TRP* 1.3 67.5 + - - +
363A THR 3.7 6.5 - - - +
364A LYS* 4.2 7.0 - - + -
448A TRP* 3.8 28.0 - - + +
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Residues in contact with TRP 329 (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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308A PRO* 4.5 0.4 - - + -
309A SER 3.1 17.9 - - - +
310A PHE* 3.9 13.9 - + + -
327A LEU* 4.0 20.0 - - + -
328A VAL* 1.3 82.8 - - - +
330A LYS* 1.3 70.3 + - - +
344A TYR* 3.5 45.9 - + + -
346A VAL* 3.8 26.7 - - + -
360A VAL* 5.1 9.6 - - + -
362A ALA 3.0 29.7 + - - -
363A THR* 3.2 33.2 + - + +
364A LYS 3.8 20.4 - - - -
365A LEU* 3.9 10.5 - - + -
378A LEU* 3.4 21.1 - - + -
448A TRP* 3.9 7.4 + - - -
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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