Contacts of the strand formed by residues 327 - 335 (chain F) in PDB entry 4LQL
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 327 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315F THR* 4.9 2.0 - - - +
318F LEU* 3.1 35.5 + - + +
319F LYS* 3.1 36.2 + - + -
321F ALA 5.5 0.2 - - - -
322F ALA* 4.3 8.9 + - - +
325F LYS* 3.6 7.6 + - - +
326F GLN* 1.3 82.0 + - - +
328F ALA* 1.3 70.4 + - - +
355F THR* 3.2 17.2 + - - -
449F VAL* 5.1 3.4 - - + -
450F LEU 3.8 5.4 - - - +
451F THR* 3.6 19.4 - - - -
452F LEU* 4.8 0.4 - - - +
453F ALA* 4.4 4.0 - - - +
454F LEU* 5.1 3.8 + - - +
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Residues in contact with ALA 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F THR* 5.4 2.0 - - - -
319F LYS* 4.2 5.8 - - - +
327F THR* 1.3 80.7 - - - +
329F LEU* 1.3 63.8 + - - +
330F MET* 5.2 4.7 - - + -
352F VAL* 6.1 0.4 - - + -
353F ASP* 3.4 33.2 - - + +
355F THR* 4.2 2.0 - - - +
356F LEU* 5.8 4.3 - - + +
449F VAL* 3.7 6.6 - - - +
450F LEU* 2.7 48.8 + - + +
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Residues in contact with LEU 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297F MET* 4.4 20.2 - - + -
303F PHE* 4.5 24.2 - - + +
305F PRO* 5.4 6.7 - - + -
311F MET* 5.2 10.3 - - + +
315F THR* 5.0 9.3 - - - -
319F LYS* 5.2 0.6 - - - +
328F ALA* 1.3 82.0 - - - +
330F MET* 1.3 92.2 + - - +
348F HIS* 5.1 11.4 - - + -
351F GLU 5.0 10.1 - - - +
352F VAL* 6.4 0.4 - - - -
353F ASP* 4.5 5.7 + - + +
447F HIS* 6.0 3.4 - - + -
448F THR 3.9 9.9 - - - +
449F VAL* 4.8 4.9 - - - +
450F LEU* 4.2 0.7 + - - +
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Residues in contact with MET 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328F ALA* 5.2 4.5 - - + -
329F LEU* 1.3 100.8 - - - +
331F GLU* 1.3 58.1 + - - +
332F ASP* 4.1 0.6 - - - +
346F GLY* 3.4 33.7 - - - +
347F SER* 3.5 8.1 - - - -
352F VAL* 4.5 19.3 - - + -
424F GLN* 3.5 21.3 - - + -
426F TRP* 3.6 29.6 - - + -
447F HIS* 3.6 1.1 - - - -
448F THR* 2.6 51.9 + - + +
450F LEU* 4.2 15.9 - - + -
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Residues in contact with GLU 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D MET* 5.4 4.6 - - - +
128D HIS* 4.0 21.2 + - + -
306F GLU* 2.7 20.5 - - - +
329F LEU* 6.0 0.4 - - + -
330F MET* 1.3 72.3 - - - +
332F ASP* 1.3 65.7 + - - +
333F TYR* 3.2 5.0 + - - +
347F SER 2.7 28.3 + - - +
348F HIS* 2.1 52.7 + - + -
446F HIS* 3.0 33.4 - - + +
447F HIS* 2.6 24.7 + - + -
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Residues in contact with ASP 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ALA* 4.6 11.4 - - + -
128D HIS* 3.0 35.7 + - + +
131D ARG* 4.7 15.2 + - - +
330F MET* 4.1 0.5 - - - +
331F GLU* 1.3 65.2 - - - +
333F TYR* 1.3 59.0 + - - +
334F THR 3.8 1.3 - - - +
344F ILE* 3.4 22.3 - - + +
346F GLY* 4.3 9.0 - - - -
426F TRP* 3.1 39.0 - - - -
446F HIS* 4.3 7.2 + - - +
448F THR* 4.0 14.2 + - - +
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Residues in contact with TYR 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D MET* 5.4 16.9 - - + +
124D HIS 5.0 1.2 - - - +
125D GLN* 4.9 10.6 - - - +
126D SER 5.4 0.6 + - - -
127D ALA* 5.4 2.5 - - - -
128D HIS* 4.3 13.2 - - + -
331F GLU 3.2 7.2 + - - +
332F ASP* 1.3 73.9 - - - +
334F THR* 1.3 70.1 + - - +
345F MET 3.4 9.5 + - - +
346F GLY* 4.3 0.2 - - - -
347F SER* 3.2 29.2 - - - +
348F HIS* 5.2 1.1 - - - +
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Residues in contact with THR 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLN* 3.5 27.4 - - - +
111D ILE* 4.1 17.0 - - + -
112D PRO* 5.3 2.5 - - + -
116D ILE* 5.9 4.9 - - + +
120D TYR* 5.2 4.3 + - + -
121D MET* 6.1 0.3 - - - -
124D HIS 4.9 5.7 + - - +
126D SER 6.1 1.3 - - - +
127D ALA* 4.8 11.0 - - - +
332F ASP 3.8 0.8 - - - -
333F TYR* 1.3 91.7 + - - +
335F LEU* 1.3 81.2 + - - +
344F ILE* 3.7 8.3 - - - +
345F MET* 3.2 31.0 + - - +
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Residues in contact with LEU 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D GLN* 4.5 5.7 + - - +
109D ASN 4.5 3.4 - - - +
110D ASN 4.0 2.1 - - - +
111D ILE* 3.2 23.8 + - - +
127D ALA* 5.1 9.8 - - + +
334F THR* 1.3 82.1 - - - +
336F ASP* 1.3 64.8 - - - +
337F LEU* 6.4 0.4 - - + -
343F ALA 3.2 14.4 - - - +
344F ILE* 5.1 2.7 - - + -
345F MET* 4.9 1.3 - - - +
432F LEU* 5.0 13.5 - - + -
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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