Contacts of the helix formed by residues 304 - 322 (chain A) in PDB entry 3SN5
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 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A GLN* 2.7 36.2 + - - +
301A MET 2.9 19.9 - - - +
302A ILE 3.2 2.2 - - - -
303A ARG* 1.3 85.9 - - - +
305A PRO* 1.4 70.0 - - + +
306A GLU* 3.2 3.8 - - + +
307A ALA* 3.2 14.6 + - + +
308A MET* 3.0 8.0 + - - +
407A PHE* 3.4 34.7 - - + +
409A TYR* 5.8 0.9 - - + -
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Residues in contact with PRO 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE 4.3 2.7 - - - +
303A ARG 3.6 9.2 - - - +
304A ASN* 1.4 83.6 - - + +
306A GLU* 1.3 57.4 + - - +
308A MET* 3.7 7.3 - - + +
309A LYS* 3.0 31.0 + - - +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ASN* 3.2 4.0 - - + -
305A PRO* 1.3 78.9 - - + +
307A ALA* 1.4 59.9 + - - +
309A LYS* 3.9 5.9 - - - +
310A ALA* 3.3 24.6 + - - +
409A TYR* 4.1 22.1 - - + -
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLN 4.4 1.3 - - - +
301A MET* 4.0 16.8 - - - +
304A ASN* 3.2 22.3 + - + +
306A GLU* 1.4 74.1 - - - +
308A MET* 1.3 64.9 + - - +
310A ALA* 3.6 1.7 + - - +
311A ALA* 3.1 26.7 + - - +
349A ILE* 3.8 9.9 - - + +
407A PHE* 4.5 2.2 - - + -
409A TYR* 3.6 37.1 - - + -
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Residues in contact with MET 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A MET* 3.3 31.8 + - - +
302A ILE* 4.5 13.7 - - + +
304A ASN 3.0 10.6 + - - +
305A PRO* 3.7 9.0 - - + +
306A GLU 3.4 0.2 - - - -
307A ALA* 1.3 76.1 - - - +
309A LYS* 1.4 54.0 + - - +
311A ALA* 3.4 2.3 + - - +
312A THR* 2.7 42.5 + - - +
462A LEU* 3.7 29.6 - - + -
465A PHE 6.0 1.1 - - - +
467A LEU* 4.4 35.7 - - + +
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PRO 3.0 17.9 + - - +
306A GLU* 3.9 6.1 - - - +
307A ALA 3.4 0.2 - - - -
308A MET* 1.4 75.5 - - - +
310A ALA* 1.4 62.3 + - - +
312A THR* 3.6 6.1 + - - -
313A GLU* 3.2 24.6 + - + +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLU 3.3 15.6 + - - +
307A ALA 3.9 1.6 - - - +
308A MET 3.3 0.2 - - - -
309A LYS* 1.4 74.4 - - - +
311A ALA* 1.3 59.6 + - - +
313A GLU* 3.4 6.5 + - - +
314A GLU* 3.0 28.2 + - - +
345A VAL* 3.9 16.3 - - + +
409A TYR* 3.7 31.2 - - + +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A MET* 3.8 26.7 - - - -
307A ALA 3.1 18.5 + - - +
308A MET 3.8 3.6 - - - +
310A ALA* 1.3 72.2 - - - +
312A THR* 1.4 59.1 + - - +
314A GLU* 3.3 4.4 + - - +
315A VAL* 3.0 34.8 + - - +
345A VAL* 3.8 8.9 - - - +
346A LEU* 4.0 11.7 - - + -
349A ILE* 3.9 11.7 - - + -
462A LEU* 4.1 4.0 - - + -
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Residues in contact with THR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 2.7 31.5 + - - +
309A LYS* 3.7 7.0 - - - -
310A ALA 3.4 0.2 - - - -
311A ALA* 1.4 74.4 - - - +
313A GLU* 1.4 58.4 + - - +
315A VAL* 3.5 2.6 + - - +
316A LYS* 2.9 33.4 + - + +
462A LEU* 3.5 27.6 - - + +
502A LYS* 5.6 7.6 - - - +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS* 3.2 15.6 + - + +
310A ALA* 3.7 6.5 - - - +
312A THR* 1.4 76.7 - - - +
314A GLU* 1.4 59.6 + - - +
316A LYS* 3.4 6.4 + - - +
317A ARG* 2.9 33.0 + - - +
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ALA 3.0 17.2 + - - +
311A ALA* 3.3 8.3 + - - +
313A GLU* 1.4 75.5 - - - +
315A VAL* 1.4 50.0 + - + +
317A ARG* 3.3 9.6 + - - +
318A THR* 2.7 41.9 + - - +
342A ASP 5.3 1.1 - - - +
343A LEU* 3.3 31.7 - - + +
344A PRO* 3.3 14.6 - - - +
345A VAL* 3.1 32.2 + - + +
346A LEU* 3.0 31.5 + - + +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA 3.0 20.8 + - - +
312A THR 4.0 3.1 - - - +
314A GLU* 1.4 70.4 - - + +
316A LYS* 1.4 60.1 + - - +
318A THR* 3.9 5.1 - - - -
319A LEU* 3.0 36.1 + - + +
343A LEU* 5.3 2.7 - - + -
346A LEU* 4.0 14.8 - - + -
459A ILE* 3.8 42.0 - - + +
462A LEU* 3.7 24.2 - - + -
463A SER* 3.7 22.9 - - - +
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Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A THR* 2.9 22.1 + - + +
313A GLU* 3.6 7.9 - - - +
315A VAL* 1.4 76.4 - - - +
317A ARG* 1.4 55.0 - - - +
319A LEU* 4.1 5.1 - - - +
320A GLU* 3.0 44.1 + - - +
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Residues in contact with ARG 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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313A GLU 2.9 18.2 + - - +
314A GLU* 3.4 8.7 - - - +
316A LYS* 1.4 72.2 - - - +
318A THR* 1.4 59.5 + - - +
320A GLU* 3.4 7.9 + - - +
321A ASN* 3.1 49.4 + - - +
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 2.7 26.7 + - - +
315A VAL* 3.9 4.5 - - - -
317A ARG* 1.4 68.6 - - - +
319A LEU* 1.3 66.9 + - - +
321A ASN* 3.5 8.6 + - - +
322A ALA* 3.1 23.2 + - - +
335A LEU* 4.4 19.7 - - + -
339A GLU* 4.1 20.4 - - + +
342A ASP 4.8 3.0 + - - +
343A LEU* 3.3 31.9 - - + +
459A ILE* 6.1 0.7 - - + -
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Residues in contact with LEU 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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315A VAL* 3.0 30.6 + - + +
316A LYS* 4.1 4.9 - - - +
318A THR* 1.3 73.8 - - - +
320A GLU* 1.4 64.7 + - + +
322A ALA* 3.3 3.1 + - - -
323A GLY 3.2 4.0 + - - -
324A GLN* 2.9 54.2 + - + +
326A VAL* 5.2 9.2 - - + +
333A ILE* 3.7 30.5 - - + -
335A LEU* 4.0 18.2 - - + -
459A ILE* 4.4 3.1 - - + -
463A SER* 3.4 28.5 - - - +
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Residues in contact with GLU 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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316A LYS* 3.0 35.1 + - - +
317A ARG* 3.7 8.1 + - - +
319A LEU* 1.4 74.8 - - - +
321A ASN* 1.4 60.8 + - - +
323A GLY* 3.1 19.6 + - - -
324A GLN 5.0 2.5 - - - +
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Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ARG* 3.1 35.2 + - - +
318A THR* 3.9 7.1 - - - +
320A GLU* 1.4 77.7 - - - +
322A ALA* 1.3 58.7 + - - +
323A GLY 3.3 1.0 + - - -
339A GLU* 5.3 0.4 - - - -
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Residues in contact with ALA 322 (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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318A THR 3.1 17.8 + - - +
319A LEU 3.9 3.6 - - - +
320A GLU 3.3 0.4 - - - -
321A ASN* 1.3 74.8 - - - +
323A GLY* 1.3 57.5 + - - +
324A GLN* 2.9 28.3 + - + +
334A CYS 4.9 0.4 - - - +
335A LEU* 3.9 15.7 - - + -
339A GLU* 3.4 35.4 - - + +
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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
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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