Contacts of the helix formed by residues 321 - 335 (chain A) in PDB entry 5M7S
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 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TRP* 3.6 10.3 - - - -
84A ARG* 5.4 2.5 - - - -
314A PRO* 3.4 23.1 - - + +
315A ASN* 2.7 65.4 + - - +
317A GLU 3.5 9.1 + - - -
318A PHE* 3.2 11.7 + - + +
319A GLU 3.2 3.0 - - - -
320A ALA* 1.3 76.8 - - - +
322A TYR* 1.3 64.4 + - - +
323A VAL 3.4 1.8 - - - -
324A ALA* 3.8 6.3 - - - +
325A ILE* 3.0 44.3 + - + +
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Residues in contact with TYR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 3.7 29.6 - - + +
87A LYS* 4.3 6.6 + - - +
88A TRP* 3.5 30.8 - + - -
319A GLU 4.0 3.9 + - - +
320A ALA 3.4 2.2 - - - -
321A ASN* 1.3 76.9 - - - +
323A VAL* 1.3 58.4 + - - +
326A HIS* 2.9 39.2 + - + +
383A ALA 3.9 9.6 - - - -
386A GLU* 2.6 35.6 + - + +
387A TRP* 3.3 69.3 - + + +
390A GLU* 4.1 20.1 + - + -
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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
----------------------------------------------------------
293A LEU* 3.1 33.7 - - + +
294A GLY 3.4 14.1 - - - +
320A ALA 4.6 2.7 + - - +
321A ASN 3.4 0.2 - - - -
322A TYR* 1.3 76.5 - - + +
324A ALA* 1.3 56.9 + - - +
327A THR* 2.7 48.3 + - + -
380A LEU* 3.8 14.1 - - + -
383A ALA* 4.2 13.9 - - + -
384A LEU* 3.5 33.2 - - + +
387A TRP* 4.2 15.4 - - + -
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Residues in contact with ALA 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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282A HIS* 3.6 52.2 + - + +
292A PHE 4.9 1.9 + - - +
294A GLY 4.8 0.2 + - - -
296A TYR* 4.9 1.0 - - - +
312A THR* 4.8 5.2 - - - +
314A PRO* 4.4 8.7 - - + -
315A ASN* 4.9 2.5 - - - +
320A ALA 4.9 1.2 + - - -
321A ASN* 3.4 22.2 + - - +
322A TYR 3.3 0.6 - - - -
323A VAL* 1.3 79.8 - - - +
325A ILE* 1.3 61.5 + - + +
327A THR* 3.5 8.1 + - - -
328A LEU* 3.5 13.3 + - - +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 3.7 25.4 - - + -
73A TRP* 5.7 1.1 - - + -
81A LEU* 3.8 19.7 - - + -
84A ARG* 6.2 2.5 - - - +
85A LEU* 3.9 11.7 - - + -
88A TRP* 3.6 25.4 - - + -
90A LEU* 3.8 19.0 - - + +
312A THR* 4.4 8.5 - - + -
314A PRO* 4.8 5.6 - - + -
318A PHE* 6.2 1.1 - - + -
321A ASN* 3.0 33.4 + - + +
324A ALA* 1.3 77.7 - - + +
326A HIS* 1.3 66.2 + - - +
328A LEU* 3.4 5.6 + - - +
329A ALA* 3.0 21.5 + - - +
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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
----------------------------------------------------------
88A TRP* 3.5 34.5 + + + -
322A TYR* 2.9 25.2 + - + +
325A ILE* 1.3 77.0 - - - +
327A THR* 1.3 58.7 + - - +
329A ALA* 3.3 5.8 + - - +
330A THR* 3.0 35.8 + - - -
379A ALA 4.6 1.8 - - - -
382A LEU* 4.0 15.5 - - + +
383A ALA* 3.3 39.9 + - + -
386A GLU* 3.5 39.0 + - + -
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Residues in contact with THR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO* 3.9 5.7 - - + +
296A TYR* 3.0 28.5 + - - -
323A VAL* 2.7 39.0 + - + +
324A ALA 3.5 4.0 + - - -
326A HIS* 1.3 71.3 - - - +
328A LEU* 1.3 63.1 + - - +
330A THR* 3.1 8.2 + - - -
331A TRP* 2.8 29.8 + - - +
374A TYR* 3.7 9.5 + - - -
379A ALA* 3.7 34.8 - - + +
380A LEU 4.0 2.2 - - - +
383A ALA* 4.0 4.9 - - + -
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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
----------------------------------------------------------
62A CYS* 4.2 18.2 - - - -
63A GLY 3.4 27.4 - - - +
90A LEU* 4.4 8.5 - - + -
296A TYR* 3.8 33.5 - - + +
310A VAL* 4.0 12.1 - - + +
312A THR* 3.7 22.0 - - + +
324A ALA 3.5 11.8 + - - +
325A ILE* 3.4 8.7 + - - +
327A THR* 1.3 80.6 + - - +
329A ALA* 1.3 63.1 + - - +
331A TRP* 3.2 24.7 + - + +
332A TYR* 3.0 21.7 + - - +
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 3.5 39.9 - - + +
90A LEU* 3.9 20.2 - - + +
325A ILE 3.0 13.0 + - - +
326A HIS 3.5 9.0 - - - +
327A THR 3.3 0.2 - - - -
328A LEU* 1.3 77.0 - - - +
330A THR* 1.3 62.1 + - - +
332A TYR* 3.4 1.2 + - - +
333A LYS* 3.0 34.4 + - - +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A HIS* 3.0 30.6 + - - -
327A THR* 3.1 11.0 + - - -
329A ALA* 1.3 75.4 - - - +
331A TRP* 1.3 61.8 + - - +
333A LYS* 3.6 14.7 + - - +
334A SER* 3.2 23.6 + - - -
374A TYR* 4.2 15.7 - - + -
379A ALA* 4.2 15.0 - - + +
382A LEU* 5.0 13.8 - - + +
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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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60A PHE* 5.0 2.7 - + - -
62A CYS* 5.1 0.9 - - - -
296A TYR* 3.6 28.0 - + + -
299A ARG* 2.9 30.4 + - + -
300A SER 3.6 17.6 + - - -
301A THR* 3.7 15.8 - - + +
303A LEU* 4.7 3.1 - - + -
304A ILE* 3.4 36.8 - - + +
307A LEU* 4.9 4.9 - - + -
310A VAL* 3.7 32.8 - - + -
327A THR 2.8 15.6 + - - +
328A LEU* 3.5 26.5 - - + +
330A THR* 1.3 71.3 - - - +
332A TYR* 1.3 83.8 + - + +
334A SER* 2.8 20.5 + - - -
374A TYR* 3.5 34.9 - + + -
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Residues in contact with TYR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.2 56.7 + + + +
62A CYS* 4.0 27.6 - - + -
89A GLU 4.3 14.8 - - - -
90A LEU* 4.3 10.8 - - + -
91A ASN* 4.6 9.5 + - - -
304A ILE* 4.2 12.7 - - + +
328A LEU 3.0 15.8 + - - +
329A ALA 3.9 3.4 - - - +
331A TRP* 1.3 85.0 - - + +
333A LYS* 1.3 68.0 + - + +
334A SER 3.2 0.9 + - - -
335A ASN 3.4 2.6 + - - -
336A MET* 3.2 58.6 + - + +
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Residues in contact with LYS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 3.0 35.5 + - - +
89A GLU* 3.4 33.2 + - + +
329A ALA* 3.0 30.7 + - - +
330A THR* 4.0 11.8 + - - +
332A TYR* 1.3 84.9 - - + +
334A SER* 1.3 61.9 + - - +
335A ASN 3.3 1.1 + - - -
336A MET* 3.8 24.8 + - - +
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Residues in contact with SER 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A THR* 3.3 19.1 - - - +
330A THR* 3.2 17.4 + - - -
331A TRP 2.8 16.8 + - - -
332A TYR 3.2 0.2 - - - -
333A LYS* 1.3 77.2 - - - +
335A ASN* 1.3 60.9 + - - +
336A MET 3.8 0.2 - - - -
373A LEU* 3.6 41.3 - - - +
374A TYR* 3.8 6.6 - - - +
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Residues in contact with ASN 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A THR* 3.0 38.6 + - - +
302A GLU* 4.4 6.1 + - - +
304A ILE* 3.6 19.2 - - + +
305A PRO* 4.0 11.8 - - - +
331A TRP 3.9 0.6 + - - -
332A TYR 3.4 5.9 + - - -
333A LYS 3.3 0.2 - - - -
334A SER* 1.3 77.8 + - - +
336A MET* 1.3 66.0 + - - +
337A ASN 3.2 19.8 + - - -
373A LEU* 3.5 25.0 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
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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