Contacts of the helix formed by residues 323 - 343 (chain A) in PDB entry 6X70
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 SER 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A TYR* 2.8 26.0 + - - -
320A PHE* 3.6 2.0 + - - -
322A HIS* 1.3 74.3 - - - +
324A ARG* 1.3 58.7 + - - +
325A LEU* 4.0 0.7 - - - +
326A HIS* 2.9 29.3 + - - +
327A HIS* 2.9 31.5 + - - -
4T C 3.6 15.7 - - - -
5T G 2.6 21.1 + - - -
6T C 4.1 5.4 - - - -
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Residues in contact with ARG 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A HIS 3.4 5.7 + - - -
323A SER* 1.3 73.0 - - - +
325A LEU* 1.3 86.3 + - + +
327A HIS* 3.6 1.4 - - - +
328A LEU* 2.9 35.1 + - + +
367A PHE* 4.1 15.8 - - + -
393A HIS* 5.0 0.2 + - - -
399A ASP* 2.8 48.6 + - - +
400A ILE 5.0 4.6 + - - -
401A ALA* 4.1 12.7 - - + +
415A GLY* 5.0 6.3 - - - +
436A TYR* 3.4 38.9 + - + +
438A PHE* 3.8 17.0 - - + -
4T C 4.3 1.4 + - - -
5T G 2.5 47.2 + - - -
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Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A SER 3.2 1.0 - - - -
324A ARG* 1.3 103.5 - - + +
326A HIS* 1.3 64.8 + - - +
328A LEU* 3.4 15.7 + - + +
329A SER* 3.1 26.9 + - - -
399A ASP* 5.5 0.2 - - - +
12P G 5.3 7.9 - - + +
5T G 3.3 38.2 + - + +
6T C 3.1 53.9 - - + +
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Residues in contact with HIS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 3.2 62.6 - + + +
323A SER* 2.9 25.7 + - - +
325A LEU* 1.3 77.2 - - - +
327A HIS* 1.3 73.2 + + - +
329A SER* 3.2 2.6 + - - -
330A ALA* 2.9 37.2 + - + +
649A TYR* 3.6 15.0 + - - -
6T C 3.4 15.0 + - - +
7T T 2.7 24.5 + - - -
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Residues in contact with HIS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE 3.2 15.5 + - - -
321A ALA* 2.7 32.2 + - - -
323A SER 2.9 27.4 + - - +
324A ARG* 3.6 6.3 - - - +
326A HIS* 1.3 80.0 - + - +
328A LEU* 1.3 57.8 + - - +
330A ALA* 3.8 2.5 - - - +
331A TRP* 2.9 69.9 + + + -
438A PHE* 3.6 33.8 - + + -
439A GLU* 5.3 4.0 - - - -
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ARG* 2.9 26.9 + - + +
325A LEU* 3.7 18.6 - - + +
326A HIS 3.2 0.2 - - - -
327A HIS* 1.3 76.4 - - - +
329A SER* 1.3 58.5 + - - +
331A TRP* 3.8 5.8 - - + +
332A LYS* 3.0 31.1 + - - +
367A PHE* 3.8 28.7 - - + -
465A SER* 5.7 5.8 - - - -
466A ILE* 3.6 31.6 + - + +
467A ASP* 5.6 1.1 - - - +
12P G 5.9 11.4 - - + +
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU 3.1 11.1 + - - -
326A HIS 3.6 2.5 - - - -
328A LEU* 1.3 77.6 - - - +
330A ALA* 1.3 57.8 + - - +
332A LYS* 3.2 18.1 + - - +
333A ALA* 2.9 29.2 + - - +
12P G 4.1 6.8 + - - +
6T C 3.0 26.0 + - - -
7T T 3.2 38.8 + - - -
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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
----------------------------------------------------------
326A HIS* 2.9 34.7 + - + +
327A HIS* 4.0 4.0 - - - +
329A SER* 1.3 75.8 - - - +
331A TRP* 1.3 60.2 + - + +
333A ALA* 3.3 6.1 + - - +
334A ASN* 2.8 43.3 + - - +
653A LYS* 6.2 1.8 - - - +
7T T 5.4 0.2 - - - -
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Residues in contact with TRP 331 (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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327A HIS* 2.9 56.2 + + + +
328A LEU* 3.8 9.9 - - + +
330A ALA* 1.3 78.5 - - + +
332A LYS* 1.3 57.0 + - - +
334A ASN* 3.4 14.0 + - - +
335A LEU* 3.0 36.2 + - + +
367A PHE* 4.2 20.2 - + - -
438A PHE* 3.4 49.4 - + + -
441A PHE* 4.0 5.8 - - + -
442A GLN* 3.6 28.0 - - + +
466A ILE* 3.3 42.6 - - + -
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Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU 3.0 17.2 + - - +
329A SER* 3.2 18.1 + - - +
331A TRP* 1.3 73.4 - - - +
333A ALA* 1.3 65.3 + - - +
335A LEU* 3.2 12.7 + - - +
336A LYS* 3.1 54.4 + - - +
464A ILE 3.8 23.3 - - - +
465A SER* 4.9 8.7 - - - +
466A ILE 5.3 0.6 - - - +
11P A 5.4 3.6 + - - -
12P G 3.9 26.0 + - - +
7T T 4.7 4.6 + - - -
8T A 4.5 18.5 + - - -
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER 2.9 16.0 + - - +
330A ALA* 3.7 7.4 - - - +
332A LYS* 1.3 78.1 - - - +
334A ASN* 1.3 61.3 + - - +
336A LYS* 3.2 10.2 + - - +
337A ASP* 2.9 29.6 + - - +
620A ARG* 3.5 29.8 - - - +
8T A 5.9 2.5 - - - -
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Residues in contact with ASN 334 (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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330A ALA* 2.8 29.2 + - - +
331A TRP* 3.7 14.6 - - + +
333A ALA* 1.3 79.7 - - - +
335A LEU* 1.3 56.3 + - + +
337A ASP* 3.5 6.2 + - - +
338A LYS* 2.9 30.2 + - - +
653A LYS* 5.5 5.2 + - - -
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TRP* 3.0 22.7 + - + +
332A LYS* 3.2 7.2 + - - +
334A ASN* 1.3 75.7 - - + +
336A LYS* 1.3 58.3 + - - +
338A LYS* 3.4 17.3 + - + +
339A PHE* 3.0 28.2 + - - +
445A SER* 4.8 4.5 - - - +
449A TYR* 3.8 32.3 - - + +
463A PRO* 3.8 20.3 - - + +
465A SER* 3.5 36.1 - - - +
466A ILE* 3.7 11.0 - - + +
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Residues in contact with LYS 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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332A LYS* 3.1 51.7 + - + +
333A ALA* 3.2 11.6 + - - +
335A LEU* 1.3 74.4 - - + +
337A ASP* 1.3 64.9 + - - +
339A PHE* 3.4 8.0 + - - +
340A LEU* 3.1 29.1 + - - +
463A PRO* 4.7 12.8 - - + +
464A ILE 5.4 0.9 - - - -
617A VAL 5.9 0.4 + - - -
618A LEU* 3.9 54.4 - - + +
8T A 4.8 16.6 + - - -
9T C 5.0 7.5 + - - +
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Residues in contact with ASP 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA 2.9 15.6 + - - +
334A ASN* 3.9 6.3 - - - +
336A LYS* 1.3 75.4 - - - +
338A LYS* 1.3 56.5 + - - +
340A LEU* 3.1 18.3 + - - +
341A ASN* 2.7 51.8 + - - +
619A GLN* 5.4 2.9 + - - -
657A ILE* 4.4 20.2 - - - +
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Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASN 2.9 19.0 + - - +
335A LEU* 3.6 18.8 - - + +
336A LYS 3.3 0.2 - - - -
337A ASP* 1.3 75.7 - - - +
339A PHE* 1.3 61.9 + - - +
341A ASN* 3.2 7.5 + - - +
342A GLU* 3.0 54.1 + - + +
449A TYR* 5.8 6.9 - - - +
453A LYS* 5.1 7.3 - - - +
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Residues in contact with PHE 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 LEU 3.0 14.2 + - - +
336A LYS 3.5 7.6 - - - +
337A ASP 3.3 0.2 - - - -
338A LYS* 1.3 76.1 - - - +
340A LEU* 1.3 70.3 + - + +
342A GLU* 3.2 7.6 + - - -
343A ASN* 2.9 58.2 + - + +
460A LEU* 3.9 25.1 - - + -
461A ILE 3.4 26.0 - - - -
462A LEU* 4.2 4.7 - - + -
463A PRO* 4.0 11.9 - - + -
614A PRO* 3.9 30.7 - - + -
615A LYS* 4.4 7.4 - - + -
618A LEU* 3.6 20.0 - - + -
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Residues in contact with LEU 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 LYS 3.1 17.4 + - - +
337A ASP* 3.1 22.2 + - - +
339A PHE* 1.3 82.4 - - + +
341A ASN* 1.3 65.4 + - - +
343A ASN 3.1 2.6 + - - -
344A ILE* 3.1 28.2 + - + +
615A LYS* 3.5 51.3 - - + +
618A LEU* 4.1 9.6 - - + +
619A GLN* 3.5 39.5 - - - +
620A ARG 5.0 0.7 - - - +
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Residues in contact with ASN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASP* 2.7 50.7 + - - +
338A LYS* 3.2 7.0 + - - +
340A LEU* 1.3 75.9 - - - +
342A GLU* 1.3 60.4 + - + +
344A ILE* 3.6 30.8 - - + +
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Residues in contact with GLU 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 LYS* 3.0 52.9 + - + +
339A PHE* 3.8 8.7 - - - +
340A LEU 3.1 0.2 - - - -
341A ASN* 1.3 79.7 - - + +
343A ASN* 1.3 69.1 + - - +
344A ILE* 3.5 3.2 + - - +
345A HIS* 4.9 1.4 + - - +
346A LYS* 4.3 16.8 + - - +
453A LYS* 4.5 14.2 + - - -
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Residues in contact with ASN 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 2.9 57.5 + - + +
340A LEU 3.1 2.7 + - - -
342A GLU* 1.3 87.2 + - - +
344A ILE* 1.3 61.4 + - - +
345A HIS 3.0 7.3 + - - +
346A LYS* 3.4 37.9 - - + +
348A THR* 4.2 13.3 + - - -
460A LEU* 5.6 1.0 - - - +
615A LYS* 3.1 27.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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