Contacts of the helix formed by residues 335 - 348 (chain A) in PDB entry 1XTG
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 LYS 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A TYR* 3.3 43.3 - - + +
333A VAL 3.5 3.2 + - - +
334A ASP* 1.3 72.1 + - - +
336A LEU* 1.3 65.4 + - + +
338A PHE* 3.5 2.3 + - - +
339A ASP* 3.1 33.4 + - - +
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Residues in contact with LEU 336 (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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334A ASP* 2.8 18.0 + - - +
335A LYS* 1.3 75.6 - - + +
337A LYS* 1.3 61.9 + - + +
339A ASP* 3.4 7.9 + - + +
340A LYS* 3.1 36.0 + - + +
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Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LEU* 4.1 36.7 - - + +
324A SER* 5.4 1.6 - - - +
334A ASP* 3.0 33.7 + - + +
336A LEU* 1.3 73.4 - - + +
338A PHE* 1.3 67.7 + - - +
340A LYS* 3.3 29.2 + - - +
341A LEU* 2.9 24.5 + - - +
162B HIS* 5.9 0.4 - - - -
163B MET* 5.8 0.9 - - + -
166B ASP* 2.7 34.9 + - - +
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Residues in contact with PHE 338 (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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283A ARG* 3.5 25.8 - - + -
286A TYR* 3.7 5.2 - - + -
287A TYR* 3.4 41.7 - + + -
290A PHE* 3.4 52.5 - + + -
321A TYR 5.9 2.5 - - - -
322A LEU* 6.4 0.2 - - - -
333A VAL* 3.9 14.1 - - + +
334A ASP 2.8 15.6 + - - +
335A LYS 3.8 3.6 - - - +
337A LYS* 1.3 76.5 - - - +
339A ASP* 1.3 63.8 + - - +
341A LEU* 3.2 7.3 + - + +
342A TYR* 2.7 67.9 + + + +
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Residues in contact with ASP 339 (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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283A ARG* 3.4 40.0 + - - +
335A LYS* 3.1 21.4 + - - +
336A LEU* 3.8 8.5 - - + +
338A PHE* 1.3 90.4 - - - +
340A LYS* 1.3 59.9 + - + +
342A TYR* 3.9 3.3 - - - +
343A LYS* 2.9 32.4 + - - +
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Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU* 3.1 24.9 + - + +
337A LYS* 3.8 32.7 - - - +
338A PHE 3.3 0.2 - - - -
339A ASP* 1.3 76.1 - - + +
341A LEU* 1.3 58.3 + - - +
343A LYS* 3.8 8.8 - - + +
344A MET* 3.0 28.2 + - - +
348A ILE* 5.6 0.3 - - - +
162B HIS* 2.7 45.1 + - + +
163B MET* 3.7 25.1 - - - +
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A SER* 5.7 0.2 - - - +
233A TYR* 4.7 9.0 - - + -
290A PHE* 4.2 25.1 - - + -
320A LYS 4.2 18.6 - - - +
321A TYR 4.2 11.2 - - - +
322A LEU* 4.2 14.6 - - + -
337A LYS 2.9 18.3 + - - +
338A PHE* 3.7 5.6 - - - +
340A LYS* 1.3 74.8 - - - +
342A TYR* 1.3 66.2 + - - +
344A MET* 3.2 11.9 + - + +
345A LEU* 3.0 43.4 + - + +
163B MET* 4.4 4.6 - - - -
167B MET* 3.8 26.2 - - + -
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Residues in contact with TYR 342 (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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235A ILE* 4.1 17.0 - - + -
264A ARG* 3.0 23.2 + - - -
279A GLU* 4.9 7.2 + - + +
282A PHE* 3.6 20.3 - - - +
283A ARG* 3.8 36.7 + - + -
286A TYR* 3.9 23.6 - + + -
290A PHE* 6.4 0.2 - + - -
338A PHE* 2.7 50.6 + + + +
339A ASP* 3.9 3.6 - - - +
341A LEU* 1.3 74.7 - - - +
343A LYS* 1.3 63.3 + - - +
345A LEU* 3.4 5.4 + - - -
346A THR* 2.8 51.3 + - + +
347A GLU* 6.6 0.2 - - - -
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Residues in contact with LYS 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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339A ASP 2.9 21.4 + - - +
340A LYS* 3.8 9.0 - - + +
342A TYR* 1.3 80.7 - - + +
344A MET* 1.3 55.8 + - - +
346A THR* 4.1 4.3 - - - -
347A GLU* 2.7 61.7 + - + +
348A ILE* 3.1 18.8 + - + -
159B ASN* 5.4 9.2 + - - +
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Residues in contact with MET 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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106A MET* 4.3 3.1 - - + -
110A SER* 3.7 12.1 - - - +
340A LYS 3.0 19.0 + - - +
341A LEU* 3.2 13.0 + - + +
343A LYS* 1.3 76.8 - - - +
345A LEU* 1.3 58.9 + - + +
348A ILE* 3.4 22.4 + - + +
349A TYR* 3.0 70.6 + - + +
160B LEU* 4.2 13.0 - - + -
163B MET* 3.7 28.5 - - + -
167B MET* 3.9 30.5 - - + -
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Residues in contact with LEU 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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107A LEU* 5.9 0.2 - - + -
110A SER* 4.4 7.9 - - - +
229A GLY* 4.8 12.1 - - - +
230A HIS* 2.8 23.8 + - + -
233A TYR* 3.8 45.3 - - + -
235A ILE* 3.9 25.6 - - + -
290A PHE* 5.8 1.8 - - + -
341A LEU* 3.0 40.6 + - + +
342A TYR* 3.9 3.6 - - - +
344A MET* 1.3 78.4 - - + +
346A THR* 1.3 59.0 + - - +
349A TYR* 3.8 37.9 - - + +
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Residues in contact with THR 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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230A HIS* 4.0 5.3 + - - +
235A ILE* 4.0 17.3 - - + -
264A ARG* 3.4 57.7 - - - +
342A TYR* 2.8 39.4 + - + +
343A LYS* 4.1 0.2 - - - -
345A LEU* 1.3 83.3 - - - +
347A GLU* 1.3 71.5 + - - +
348A ILE 3.9 0.2 - - - -
349A TYR 4.5 1.0 - - - +
350A THR* 3.6 15.8 - - - +
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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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279A GLU* 3.6 24.6 - - - +
342A TYR* 6.6 0.2 - - - -
343A LYS* 2.7 51.8 + - + +
346A THR* 1.3 87.6 - - - +
348A ILE* 1.3 62.3 + - + +
350A THR* 3.3 14.1 - - - +
353A ASN* 3.5 9.7 + - - -
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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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103A LEU* 3.7 22.3 - - + +
340A LYS 5.6 0.4 - - - +
343A LYS* 3.1 20.5 + - + +
344A MET* 3.5 35.7 - - + +
347A GLU* 1.3 77.1 - - + +
349A TYR* 1.3 64.4 + - + +
350A THR 3.0 5.4 + - - -
353A ASN* 3.0 26.7 + - - +
156B ILE* 3.9 20.0 - - + -
159B ASN* 4.1 30.5 - - + +
160B LEU* 3.9 14.8 - - + -
163B MET* 5.7 2.0 - - + -
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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