Contacts of the helix formed by residues 316 - 330 (chain A) in PDB entry 4X8G
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 ASN 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A GLU* 1.3 92.8 + - + +
317A GLU* 1.3 60.3 + - - +
318A ASP* 3.1 12.6 - - - -
319A PHE* 2.9 34.5 + - + +
320A LEU* 3.1 24.3 + - - +
632A ASP* 4.1 25.5 + - + +
635A THR* 4.6 12.5 - - + +
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Residues in contact with GLU 317 (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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314A PHE 3.1 18.8 + - - +
315A GLU* 2.9 38.0 + - - +
316A ASN* 1.3 77.8 + - - +
318A ASP* 1.3 60.8 + - - +
320A LEU* 3.5 25.1 + - + +
321A LYS* 3.6 6.6 + - - +
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Residues in contact with ASP 318 (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 ASN* 3.5 14.6 - - - +
317A GLU* 1.3 75.8 - - - +
319A PHE* 1.3 71.1 + - - +
321A LYS* 3.3 21.3 - - - +
322A SER* 3.3 8.1 + - - -
631A ASN* 4.0 22.0 - - - +
632A ASP* 5.3 1.4 - - - +
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Residues in contact with PHE 319 (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 ASN* 2.9 30.9 + - + +
318A ASP* 1.3 81.5 + - - +
320A LEU* 1.3 59.3 + - - +
321A LYS 3.1 1.3 - - - -
322A SER* 2.8 24.7 + - - +
323A VAL* 2.8 25.7 + - + +
630A ILE* 4.1 11.9 - - + -
631A ASN* 5.5 2.7 - - + +
632A ASP* 4.1 17.7 - - + +
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Residues in contact with LEU 320 (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 ALA* 5.9 5.4 - - + -
311A CYS 6.0 6.7 - - - +
315A GLU 4.2 7.0 - - - +
316A ASN* 3.1 41.9 + - - +
317A GLU* 3.5 15.9 - - + +
318A ASP 3.3 0.2 - - - -
319A PHE* 1.3 76.9 - - - +
321A LYS* 1.3 57.3 + - - +
323A VAL* 3.6 7.5 - - + +
324A THR* 2.8 39.4 + - + +
336A ILE* 4.6 25.6 - - + -
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Residues in contact with LYS 321 (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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317A GLU 3.6 5.8 + - - +
318A ASP* 3.3 15.2 + - - +
319A PHE 3.1 0.2 - - - -
320A LEU* 1.3 78.7 - - - +
322A SER* 1.3 58.9 + - - +
324A THR* 2.7 20.3 + - - -
325A THR* 2.9 25.3 + - + +
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASP 3.3 6.3 + - - -
319A PHE* 2.8 28.3 + - - -
321A LYS* 1.3 79.8 - - - +
323A VAL* 1.3 57.8 + - - +
325A THR* 2.7 21.1 + - - -
326A LEU* 3.6 11.4 + - - +
628A THR* 4.8 12.9 - - - +
629A PHE 5.5 2.0 - - - -
630A ILE* 4.0 27.9 - - - +
631A ASN 5.3 1.1 + - - -
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Residues in contact with VAL 323 (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 VAL* 5.0 10.8 - - + -
310A ALA* 5.3 7.6 - - + -
316A ASN* 6.3 0.2 - - - +
319A PHE* 2.8 23.8 + - + +
320A LEU* 3.6 8.5 - - + +
321A LYS 3.1 0.2 - - - -
322A SER* 1.3 76.8 - - - +
324A THR* 1.3 65.1 + - + +
325A THR 3.2 0.2 - - - -
326A LEU* 3.2 16.4 + - - +
327A ALA* 3.2 12.5 + - - +
334A LEU* 3.7 20.9 - - + -
590A LEU* 5.4 7.6 - - + -
592A LEU* 5.8 0.5 - - - +
630A ILE* 4.2 21.3 - - + -
647A THR* 5.2 15.0 - - + +
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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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320A LEU* 2.8 22.3 + - + +
321A LYS* 2.7 24.9 + - - -
323A VAL* 1.3 75.6 - - + +
325A THR* 1.3 61.4 + - - +
327A ALA* 4.1 0.9 - - - +
328A MET* 3.1 24.9 + - - +
334A LEU* 3.7 29.6 - - + -
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Residues in contact with THR 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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321A LYS* 2.9 19.6 + - + +
322A SER* 2.7 30.2 + - - -
324A THR* 1.3 80.3 - - - +
326A LEU* 1.3 56.4 + - - +
328A MET* 3.5 5.0 + - - +
329A LYS* 2.9 29.5 + - - +
628A THR* 5.3 4.7 - - - +
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Residues in contact with LEU 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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322A SER 3.8 9.2 - - - +
323A VAL* 3.2 11.1 + - - +
325A THR* 1.3 79.6 + - - +
327A ALA* 1.3 59.8 + - - +
329A LYS* 3.3 5.2 + - + +
330A ALA* 2.9 30.1 + - - +
590A LEU* 4.6 11.0 - - + +
592A LEU* 4.5 18.1 - - + +
595A HIS* 3.7 29.5 + - + +
596A LEU 3.3 35.4 - - - +
597A GLY* 3.9 10.3 - - - +
626A GLN 5.1 0.2 - - - +
628A THR* 3.6 23.1 - - + +
630A ILE* 5.8 4.0 - - + -
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Residues in contact with ALA 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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308A VAL* 4.8 4.3 - - + -
323A VAL 3.2 4.1 + - - +
324A THR 4.1 2.5 - - - +
326A LEU* 1.3 79.5 - - - +
328A MET* 1.3 57.3 + - - +
330A ALA* 3.5 1.0 + - - +
331A LYS 3.1 7.3 + - - -
332A CYS* 2.7 52.7 + - + +
334A LEU* 3.6 34.5 - - + -
592A LEU* 4.5 14.8 - - + +
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Residues in contact with MET 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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324A THR 3.1 18.9 + - - +
325A THR* 3.9 5.4 - - - +
326A LEU 3.3 0.2 - - - -
327A ALA* 1.3 77.8 - - - +
329A LYS* 1.3 60.2 + - - +
331A LYS* 3.6 9.7 + - - +
332A CYS 4.9 1.1 - - - -
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Residues in contact with LYS 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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325A THR 2.9 18.9 + - - +
326A LEU* 3.6 7.2 - - + +
327A ALA 3.2 0.2 - - - -
328A MET* 1.3 76.0 - - - +
330A ALA* 1.3 58.1 + - - +
331A LYS* 3.1 8.1 + - - +
595A HIS* 3.1 29.8 - - + +
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Residues in contact with ALA 330 (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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305A PRO* 5.8 3.0 - - + +
326A LEU 2.9 14.8 + - - +
327A ALA* 4.3 2.9 - - - +
328A MET 3.4 0.2 - - - -
329A LYS* 1.3 75.4 - - - +
331A LYS* 1.3 70.5 + - - +
332A CYS* 3.4 6.4 - - + +
592A LEU* 3.5 31.0 - - + +
594A LYS 6.0 0.2 - - - +
595A HIS* 3.4 20.2 - - + +
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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