Contacts of the helix formed by residues 335 - 353 (chain A) in PDB entry 4R2G
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 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ILE 3.5 1.0 + - - -
334A SER* 1.3 72.2 + - - +
336A ALA* 1.3 55.3 + - - +
338A TRP* 4.6 0.9 - - - -
339A ASN* 2.5 53.0 + - - +
389A GLN* 4.4 16.8 + - - +
403A GLY 5.4 1.8 + - - -
404A THR* 3.4 22.5 + - - +
405A GLU* 3.9 2.8 + - - +
410A GLY* 3.4 21.5 - - - +
411A ASN* 2.6 55.3 + - - +
412A ASP 3.1 9.1 + - - +
414A ILE* 3.6 38.7 - - + +
1U NAG 3.4 24.5 - - - +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A SER* 3.4 10.7 + - - +
335A ARG* 1.3 76.8 - - - +
337A GLN* 1.3 57.2 + - + +
339A ASN* 2.8 5.9 + - - +
340A ASN* 2.7 45.2 + - - +
1U NAG 3.4 23.8 - - - -
2U NAG 5.2 2.7 - - - +
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Residues in contact with GLN 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A SER 5.1 4.8 + - - +
292A VAL* 3.6 22.1 - - + +
293A LYS* 3.8 39.9 + - - +
334A SER* 3.8 23.0 + - - +
336A ALA* 1.3 82.2 - - + +
338A TRP* 1.3 58.9 + - - +
340A ASN* 3.5 9.0 + - - +
341A THR* 2.8 32.2 + - - -
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Residues in contact with TRP 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 3.9 12.6 - - + -
288A LEU* 5.9 0.2 - - + -
292A VAL* 4.2 11.3 - - + +
333A ILE* 4.2 9.9 - - + -
334A SER 3.3 18.0 + - - +
335A ARG* 4.3 2.9 - - - +
336A ALA 3.2 0.6 - - - -
337A GLN* 1.3 78.9 - - - +
339A ASN* 1.3 63.7 + - - +
341A THR* 3.2 14.6 + - + -
342A LEU* 2.9 51.4 + - + +
389A GLN 5.4 0.7 - - - -
390A LEU* 2.9 50.7 + - + +
391A PHE* 3.6 24.7 - + - -
414A ILE* 4.5 9.4 - - + -
449A ILE* 4.1 28.3 - - + -
452A LEU* 3.9 30.5 - - + -
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Residues in contact with ASN 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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335A ARG* 2.5 28.9 + - - +
336A ALA 2.8 3.1 + - - +
338A TRP* 1.3 80.9 - - - +
340A ASN* 1.3 62.3 + - - +
342A LEU* 3.4 9.6 + - - +
343A LYS* 3.3 19.2 + - - +
404A THR* 3.8 18.8 + - - +
414A ILE* 5.6 0.2 - - - +
1U NAG 1.3 92.1 + - + +
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Residues in contact with ASN 340 (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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336A ALA* 2.7 29.6 + - - +
337A GLN* 3.8 8.0 - - - +
339A ASN* 1.3 70.7 - - - +
341A THR* 1.3 65.9 + - - +
343A LYS* 3.0 34.0 + - - +
344A GLN* 3.1 28.5 + - - +
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Residues in contact with THR 341 (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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288A LEU* 3.9 25.4 - - + -
290A GLU* 4.7 7.3 + - - +
292A VAL* 3.1 18.1 - - + +
337A GLN 2.8 23.4 + - - -
338A TRP* 3.2 21.5 + - + +
340A ASN* 1.3 76.3 - - - +
342A LEU* 1.3 63.6 + - + +
344A GLN* 3.3 13.4 + - + +
345A ILE* 3.0 40.6 + - + +
452A LEU* 5.1 0.2 - - + -
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Residues in contact with LEU 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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338A TRP* 2.9 56.2 + - + +
339A ASN* 3.7 7.0 - - - +
340A ASN 3.2 0.2 - - - -
341A THR* 1.3 76.9 - - + +
343A LYS* 1.3 58.9 + - - +
345A ILE* 3.2 14.3 + - + +
346A VAL* 2.8 34.0 + - - +
361A PHE* 3.8 27.5 - - + -
390A LEU 3.8 9.4 - - - +
391A PHE* 5.1 3.1 - - + -
393A SER* 3.9 14.6 - - - +
395A TRP* 3.4 28.3 - - + -
404A THR* 4.7 5.6 - - + -
452A LEU* 5.5 1.1 - - + -
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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
----------------------------------------------------------
339A ASN 3.3 8.1 + - - +
340A ASN* 3.0 28.9 + - - +
342A LEU* 1.3 79.3 - - - +
344A GLN* 1.3 59.5 + - + +
346A VAL* 3.1 10.0 + - - +
347A GLU* 3.0 27.0 + - - +
395A TRP* 4.0 11.6 - - + -
398A THR* 3.5 38.6 - - - +
399A GLU* 4.7 14.4 + - - +
1U NAG 6.3 1.1 - - + -
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Residues in contact with GLN 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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270A VAL* 3.3 33.0 - - + +
288A LEU* 5.7 0.5 - - - +
289A ASN* 3.9 14.8 + - - +
290A GLU* 4.3 21.3 + - - +
340A ASN* 3.1 24.5 + - - +
341A THR* 3.6 13.1 + - + +
343A LYS* 1.3 79.6 - - + +
345A ILE* 1.3 61.0 + - - +
347A GLU* 3.6 23.4 + - - +
348A LYS* 3.7 13.0 + - - +
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Residues in contact with ILE 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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270A VAL* 4.5 8.5 - - + -
272A ILE* 4.8 4.7 - - + -
286A VAL* 3.9 31.9 - - + -
288A LEU* 4.0 9.9 - - + -
341A THR* 3.0 37.6 + - + +
342A LEU* 3.7 11.4 - - + +
344A GLN* 1.3 76.5 - - + +
346A VAL* 1.3 66.2 + - - +
347A GLU 3.2 0.2 - - - -
348A LYS* 3.3 3.9 + - - +
349A LEU* 2.9 43.0 + - + +
361A PHE* 4.5 9.2 - - + -
452A LEU* 4.1 21.1 - - + -
454A LEU* 4.7 9.9 - - + -
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Residues in contact with VAL 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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342A LEU 2.8 21.4 + - - +
343A LYS* 3.2 11.2 - - - +
345A ILE* 1.3 76.9 - - - +
347A GLU* 1.3 55.3 + - - +
350A ARG* 2.9 54.1 + - - +
359A ILE* 3.5 21.3 - - + -
361A PHE* 4.0 5.6 - - + -
395A TRP* 3.5 36.8 - - + -
398A THR* 3.6 26.9 - - + +
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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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343A LYS 3.0 10.7 + - - +
344A GLN* 3.6 18.1 - - - +
345A ILE 3.2 0.2 - - - -
346A VAL* 1.3 76.7 - - - +
348A LYS* 1.3 68.7 + - + +
350A ARG* 4.1 3.4 + - - +
351A GLU* 3.2 24.4 + - - +
398A THR* 4.4 16.2 - - + +
517A NAG 5.9 2.7 - - - +
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Residues in contact with LYS 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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232A THR* 5.8 3.2 - - - +
269A LYS* 3.7 31.4 - - + +
270A VAL* 3.4 35.4 - - + +
271A VAL* 4.7 6.5 - - - +
272A ILE* 3.6 28.6 - - + +
344A GLN 3.7 11.9 + - - +
345A ILE 3.3 6.2 + - - +
347A GLU* 1.3 80.0 - - + +
349A LEU* 1.3 59.4 + - - +
351A GLU* 3.0 40.8 + - - +
352A GLN* 2.9 30.9 + - - +
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Residues in contact with LEU 349 (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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272A ILE* 3.7 18.8 - - + -
284A ILE* 4.6 7.9 - - + -
286A VAL* 6.3 0.4 - - + -
345A ILE* 2.9 36.5 + - + +
348A LYS* 1.3 77.6 - - - +
350A ARG* 1.3 57.0 + - - +
352A GLN 3.2 1.0 + - - -
353A PHE* 2.8 45.6 + - + +
359A ILE* 3.8 24.5 - - + -
361A PHE* 4.3 9.6 - - + -
454A LEU* 4.9 5.6 - - + -
468A PHE* 3.6 54.3 - - + -
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Residues in contact with ARG 350 (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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346A VAL* 2.9 38.5 + - - +
347A GLU* 4.3 3.0 + - - +
349A LEU* 1.3 74.0 - - - +
351A GLU* 1.3 60.4 + - - +
353A PHE* 4.4 2.9 - - - +
354A ASN* 2.8 9.6 + - - -
356A ASN* 2.6 71.0 + - - +
357A LYS 3.7 19.5 + - - +
359A ILE* 4.1 13.5 - - + -
395A TRP 4.8 2.0 - - - -
396A ASN 3.6 23.4 + - - -
397A ASP* 4.1 16.8 + - - +
398A THR* 3.8 12.3 - - - +
517A NAG 3.5 33.7 + - - +
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Residues in contact with GLU 351 (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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269A LYS* 5.3 1.7 + - - -
347A GLU* 3.2 17.1 + - - +
348A LYS* 3.0 47.6 + - - +
349A LEU 3.2 0.2 - - - -
350A ARG* 1.3 76.7 - - - +
352A GLN* 1.3 81.0 + - - +
353A PHE 3.5 0.3 + - - -
354A ASN* 3.6 12.7 + - - +
356A ASN* 5.0 1.6 - - - -
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Residues in contact with GLN 352 (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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272A ILE* 4.6 9.2 - - + +
277A PHE* 3.6 54.9 - - + +
348A LYS* 2.9 17.2 + - - +
349A LEU 3.7 3.6 - - - +
351A GLU* 1.3 95.0 - - - +
353A PHE* 1.3 72.2 + - + +
354A ASN* 3.4 7.0 + - - +
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Residues in contact with PHE 353 (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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277A PHE* 4.4 25.8 - + + -
278A THR* 6.0 0.2 - - - -
284A ILE* 4.6 1.1 - - + -
349A LEU* 2.8 36.5 + - + +
350A ARG* 3.6 2.0 - - - +
352A GLN* 1.3 89.2 - - + +
354A ASN* 1.3 72.2 + - - +
356A ASN 3.4 1.8 - - - -
357A LYS* 3.1 25.8 - - + +
359A ILE* 5.6 1.6 - - + -
456A ARG* 3.0 51.4 - - - -
466A GLU* 3.9 27.6 - - + -
468A PHE* 3.6 22.0 - + - -
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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