Contacts of the helix formed by residues 316 - 332 (chain A) in PDB entry 3MOS
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 ALA 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ILE* 1.3 80.3 - - - +
317A THR* 1.3 65.6 + - - +
318A ARG* 3.1 13.9 - - + +
319A LYS* 3.1 16.1 + - + +
320A ALA* 3.1 9.7 + - - +
473A SER 3.6 8.1 - - - +
474A ARG 3.2 27.8 - - - +
475A PRO 3.4 14.1 - - - +
476A GLU* 3.7 13.0 - - + +
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Residues in contact with THR 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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315A ILE 3.7 1.3 + - - +
316A ALA* 1.3 73.1 - - - +
318A ARG* 1.3 57.5 + - - +
320A ALA* 4.1 4.3 - - - -
321A TYR 2.9 22.9 + - - -
448A PRO* 3.6 20.7 + - - +
449A SER 3.8 4.0 - - - +
450A ASP* 3.7 25.4 - - - +
451A GLY 5.3 0.2 - - - +
454A THR* 3.2 25.2 - - - +
472A THR* 3.4 17.7 - - - +
473A SER* 2.9 38.1 + - - +
475A PRO 4.5 1.4 + - - -
477A ASN* 6.5 0.4 - - + -
509A GLY* 6.0 0.9 - - - -
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Residues in contact with ARG 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 ALA* 4.0 7.8 - - + +
317A THR* 1.3 76.0 + - - +
319A LYS* 1.3 64.0 + - - +
321A TYR* 3.4 8.8 + - - +
322A GLY 3.4 4.0 + - - -
344A ASN 4.6 0.4 + - - -
345A SER* 2.9 37.9 + - - +
346A THR 3.1 21.2 - - - +
347A PHE* 3.6 23.1 - - + +
415A SER* 4.1 10.5 - - - -
416A HIS* 3.5 21.4 + - - -
472A THR* 3.7 21.0 - - - +
473A SER 3.2 20.6 + - - +
474A ARG* 3.9 43.3 + - - +
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 3.9 16.2 - - + -
316A ALA* 3.1 14.7 + - + +
318A ARG* 1.3 79.0 - - + +
320A ALA* 1.3 64.5 + - - +
321A TYR 3.1 1.6 - - - -
322A GLY* 3.1 3.6 + - - -
323A GLN* 3.0 43.9 + - - +
347A PHE* 3.6 44.8 - - + -
350A ILE* 4.2 4.3 - - + +
476A GLU* 6.6 0.2 - - - -
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Residues in contact with ALA 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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309A TYR* 3.5 21.0 + - + +
315A ILE* 4.2 4.2 - - + +
316A ALA 3.1 11.0 + - - +
317A THR* 3.3 7.6 + - - +
319A LYS* 1.3 75.4 - - - +
321A TYR* 1.3 59.0 + - - +
323A GLN* 3.7 1.7 - - - +
324A ALA* 2.8 31.4 + - - +
451A GLY* 3.5 33.2 - - - +
454A THR* 3.7 12.6 - - - +
455A GLU* 5.2 0.5 + - - +
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Residues in contact with TYR 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 THR 2.9 13.1 + - - +
318A ARG 3.5 7.9 - - - +
319A LYS 3.1 0.2 - - - -
320A ALA* 1.3 78.4 - - - +
322A GLY* 1.3 55.2 + - - +
324A ALA* 3.3 3.1 + - - +
325A LEU* 2.8 57.5 + - + +
346A THR 3.6 17.3 - - - -
348A SER* 4.6 5.6 - - - -
385A PHE* 3.5 38.0 + + - +
386A CYS 4.2 5.9 + - - -
387A SER* 4.2 16.6 + - - -
413A CYS* 3.4 41.1 - - + +
454A THR* 3.6 8.5 - - + +
458A VAL* 3.5 22.9 - - + -
470A ILE* 4.5 6.5 - - + -
472A THR* 4.0 11.7 - - + -
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Residues in contact with GLY 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ARG 3.4 4.4 + - - -
319A LYS 3.1 7.1 + - - -
321A TYR* 1.3 80.6 - - - +
323A GLN* 1.3 63.7 + - - +
325A LEU* 3.9 3.9 - - - +
326A ALA* 3.0 24.8 + - - +
347A PHE* 3.0 33.6 - - - +
348A SER* 4.5 1.8 - - - -
350A ILE* 3.8 9.2 - - - +
351A PHE 4.4 1.6 + - - -
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Residues in contact with GLN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A TYR* 2.7 33.9 + - - +
315A ILE* 3.4 17.4 - - - +
319A LYS* 3.0 36.5 + - - +
320A ALA 3.7 3.6 - - - +
322A GLY* 1.3 78.0 - - - +
324A ALA* 1.3 57.7 + - - +
326A ALA* 3.7 2.4 - - - +
327A LYS* 2.9 30.1 + - - +
350A ILE* 3.8 20.8 - - + +
455A GLU* 5.5 1.1 - - - +
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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
----------------------------------------------------------
303A MET* 3.4 6.4 - - + +
320A ALA 2.8 21.9 + - - +
321A TYR 3.8 3.1 - - - +
323A GLN* 1.3 74.8 - - - +
325A LEU* 1.3 58.5 + - - +
327A LYS* 3.3 6.3 + - - +
328A LEU* 2.8 30.0 + - - +
455A GLU* 3.6 43.0 + - + +
458A VAL* 3.9 15.9 - - + -
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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
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321A TYR* 2.8 48.1 + - + +
322A GLY* 3.9 3.6 - - - +
324A ALA* 1.3 78.1 - - - +
326A ALA* 1.3 56.4 + - - +
328A LEU* 3.2 3.8 + - + +
329A GLY 2.9 24.6 + - - -
335A ILE* 4.0 17.5 - - + -
337A ALA* 3.9 24.9 - - + -
348A SER* 4.6 9.2 - - - -
351A PHE* 3.4 22.9 - - + -
385A PHE* 3.8 35.0 - - + +
458A VAL* 4.2 10.0 - - + +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLY 3.0 17.9 + - - +
323A GLN 3.7 3.4 - - - +
325A LEU* 1.3 74.4 - - - +
327A LYS* 1.3 63.4 + - - +
329A GLY 3.0 3.8 + - - -
330A HIS* 3.2 8.2 - - - -
350A ILE* 3.7 19.5 - - + -
351A PHE* 3.9 22.8 - - - +
354A GLU* 3.7 20.2 - - + +
355A HIS* 2.9 22.2 + - - -
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Residues in contact with LYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET* 3.7 11.0 - - - -
304A PRO* 3.7 25.7 - - + +
305A SER* 3.0 19.9 + - - +
306A LEU 2.9 24.2 + - - -
307A PRO* 3.9 2.4 - - - +
308A SER* 4.6 6.8 + - - +
323A GLN 2.9 18.8 + - - +
324A ALA* 3.5 5.8 - - - +
326A ALA* 1.3 74.9 - - - +
328A LEU* 1.3 62.7 + - - +
330A HIS* 3.0 26.7 + - + +
331A ALA 3.6 3.5 + - - -
354A GLU* 5.5 0.2 - - - -
455A GLU* 2.8 36.9 + - - +
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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
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301A ILE* 3.6 26.0 - - + +
302A ARG 4.2 2.7 - - - +
303A MET* 3.8 38.1 - - + +
324A ALA 2.8 17.3 + - - +
325A LEU* 3.2 8.0 + - + +
327A LYS* 1.3 77.6 - - - +
329A GLY* 1.3 58.5 + - - +
331A ALA* 3.0 17.0 + - + +
332A SER 3.4 8.3 + - - -
335A ILE* 3.8 22.1 - - + +
385A PHE* 4.6 2.9 - - + -
458A VAL* 4.1 19.1 - - + +
459A GLU* 4.7 2.9 - - + -
462A ALA* 3.6 30.1 - - + -
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Residues in contact with GLY 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 LEU 2.9 14.1 + - - -
326A ALA 3.0 1.2 + - - -
328A LEU* 1.3 76.8 - - - +
330A HIS* 1.3 56.1 + - - +
332A SER 3.0 21.6 + - - +
333A ASP* 5.0 0.3 - - - +
335A ILE* 4.4 3.5 - - - +
351A PHE* 3.9 13.9 - - - -
355A HIS* 3.4 21.8 - - - -
358A ARG* 3.0 19.0 + - - -
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Residues in contact with HIS 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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304A PRO* 5.0 10.4 - - + +
326A ALA 3.2 23.3 + - - -
327A LYS* 3.0 13.7 + - + +
329A GLY* 1.3 76.0 - - - +
331A ALA* 1.3 61.1 + - - +
332A SER 3.4 0.4 - - - -
354A GLU* 2.8 31.7 + - + -
355A HIS* 3.4 18.0 - + - -
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 4.5 4.0 - - + +
302A ARG 3.0 30.3 - - - +
304A PRO* 4.1 17.5 - - + -
327A LYS 3.6 2.4 + - - -
328A LEU* 3.0 15.3 + - + +
330A HIS* 1.3 80.5 - - - +
332A SER* 1.3 59.5 + - - +
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 3.7 36.0 - - - +
328A LEU 3.4 2.0 + - - -
329A GLY 3.0 10.4 - - - +
330A HIS 3.4 1.4 - - - -
331A ALA* 1.3 83.0 - - - +
333A ASP* 1.3 59.1 + - - +
334A ARG* 3.0 29.3 + - - +
335A ILE* 3.7 10.7 + - - +
358A ARG* 2.9 18.4 + - - -
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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
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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