Contacts of the strand formed by residues 342 - 348 (chain A) in PDB entry 1HLG
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 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ILE* 3.3 20.9 - - + +
318A VAL* 3.8 19.3 - - + -
336A LEU* 3.8 42.2 - - + +
339A LEU* 3.6 19.9 + - + +
341A ASN* 1.3 75.3 - - - +
343A ILE* 1.3 60.4 + - - +
344A TYR 3.0 30.1 - - - +
345A HIS* 4.7 7.6 - - + +
364B GLN* 4.5 27.3 - - + +
368B ASN* 4.1 12.6 + - - -
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Residues in contact with ILE 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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175A THR* 4.1 26.2 - - + +
315A PRO* 4.0 14.8 - - + -
316A ILE 2.9 17.6 + - - +
317A ALA* 4.3 6.1 - - + -
341A ASN* 3.5 25.4 - - - +
342A LEU* 1.3 73.5 - - - +
344A TYR* 1.3 68.5 + - + +
373A MET* 5.3 9.0 - - + -
377A ASP* 6.1 0.4 - - - +
364B GLN 5.7 0.2 - - - -
368B ASN* 4.6 19.1 - - - +
369B ASP* 5.0 0.5 - - - +
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Residues in contact with TYR 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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316A ILE 3.7 0.8 + - - -
317A ALA* 4.0 12.3 - - + -
318A VAL 3.1 14.6 + - - -
319A TRP* 3.8 35.4 - + - -
342A LEU* 3.0 24.7 + - - +
343A ILE* 1.3 85.3 - - + +
345A HIS* 1.3 74.4 + - - +
346A LYS* 3.5 39.9 - - + +
369A ASP* 3.8 11.7 + - - -
373A MET* 4.1 20.4 - - + -
344B TYR* 3.2 20.8 + + - -
364B GLN 4.8 7.2 + - - -
369B ASP* 3.5 35.0 - - + -
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Residues in contact with HIS 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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318A VAL* 3.3 17.9 - - + -
320A ASN* 2.9 29.5 + - - -
336A LEU* 2.9 36.7 - - + +
342A LEU* 4.7 11.8 - - + +
344A TYR* 1.3 86.3 - - - +
346A LYS* 1.3 81.3 + - - +
347A GLU* 4.2 12.4 + - + +
346B LYS* 2.7 34.7 + - - +
364B GLN* 4.3 10.9 + - + +
365B GLU* 3.0 32.3 + - - +
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Residues in contact with LYS 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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318A VAL 3.0 4.9 + - - -
319A TRP* 3.2 17.5 - - + +
320A ASN* 3.1 23.6 + - - +
344A TYR* 3.5 30.0 - - + +
345A HIS* 1.3 81.5 - - - +
347A GLU* 1.3 66.5 + - - +
348A ILE* 4.0 9.9 + - + +
364A GLN 4.8 2.6 + - - -
365A GLU* 3.3 50.2 + - - +
369A ASP* 4.6 7.2 + - - +
344B TYR* 5.2 3.6 - - + +
345B HIS 4.2 18.9 + - - -
346B LYS* 4.1 21.5 - - + +
347B GLU 5.9 0.7 - - - +
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Residues in contact with GLU 347 (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* 3.3 40.5 + - - +
322A GLY* 3.7 24.1 - - - +
329A PRO* 4.1 14.7 - - - +
345A HIS* 4.2 11.9 + - + +
346A LYS* 1.3 77.7 - - - +
348A ILE* 1.3 60.7 + - - +
349A PRO* 3.1 15.9 - - + +
346B LYS* 5.2 3.1 - - - +
347B GLU 4.1 13.5 + - - +
349B PRO* 3.5 40.8 - - + +
350B PHE* 4.7 5.7 - - - -
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Residues in contact with ILE 348 (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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319A TRP* 4.8 2.7 - - + -
320A ASN 2.9 9.6 + - - +
321A GLY* 3.4 2.6 - - - -
322A GLY 2.9 20.6 + - - -
346A LYS* 4.1 16.2 - - + +
347A GLU* 1.3 72.5 - - - +
349A PRO* 1.4 68.3 - - + +
350A PHE* 4.3 3.4 - - + +
351A TYR* 3.2 50.6 + - + +
356A PHE* 4.4 4.0 - - + -
365A GLU* 3.0 52.3 - - + +
366A VAL* 3.6 21.8 - - + -
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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