Contacts of the helix formed by residues 321 - 340 (chain A) in PDB entry 1M2V
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 HIS 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.5 28.5 - - + +
299A ILE 3.5 27.4 - - - +
300A VAL* 3.8 10.3 - - + -
301A ASN* 3.0 42.1 + - - -
306A ASP* 3.1 10.6 + - - -
307A PRO 5.9 0.4 - - - -
319A ALA 3.4 0.2 - - - -
320A GLN* 1.3 110.9 + - + +
322A TYR* 1.3 66.2 + - - +
323A LYS 3.4 2.4 + - - -
324A LYS* 3.4 17.5 + - + +
325A ALA* 3.2 22.2 + - - +
357A GLU* 5.5 0.2 - - - -
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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
----------------------------------------------------------
299A ILE 5.2 0.4 + - - -
309A ARG* 4.0 9.7 - - + +
314A ILE* 3.7 43.9 - - + +
319A ALA* 3.6 23.3 - - + +
320A GLN 3.6 0.4 - - - -
321A HIS* 1.3 77.4 - - - +
323A LYS* 1.3 65.9 + - + +
325A ALA* 3.4 2.8 + - - +
326A CYS* 2.9 52.3 + - - -
356A SER* 2.8 33.3 + - - -
357A GLU* 3.1 44.8 + - + +
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Residues in contact with LYS 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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317A ASP* 2.9 30.3 + - - +
319A ALA 4.5 5.2 + - - +
320A GLN 5.2 1.4 + - - +
321A HIS 3.5 1.0 - - - -
322A TYR* 1.3 83.3 - - + +
324A LYS* 1.3 62.0 + - + +
326A CYS* 4.0 4.1 - - - +
327A LYS* 3.0 28.8 + - - +
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Residues in contact with LYS 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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298A LEU* 6.5 0.4 - - + -
320A GLN* 3.1 27.9 + - - +
321A HIS* 3.4 15.1 + - - +
323A LYS* 1.3 75.7 - - + +
325A ALA* 1.3 56.2 + - - +
327A LYS* 3.1 9.7 + - - +
328A PHE* 2.7 36.9 + - - +
331A GLN* 5.4 0.2 + - - -
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Residues in contact with ALA 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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297A GLY* 4.8 3.6 - - - -
298A LEU 3.9 17.9 - - - +
299A ILE* 4.1 8.3 - - + -
321A HIS 3.2 15.9 + - - +
322A TYR* 3.4 5.6 - - - +
324A LYS* 1.3 75.2 - - - +
326A CYS* 1.3 60.3 + - - +
328A PHE* 2.8 21.7 + - - +
329A TYR* 2.8 27.8 + - + -
357A GLU* 3.8 20.4 - - + -
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Residues in contact with CYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 2.9 61.1 + - - +
323A LYS* 4.0 4.9 - - - +
325A ALA* 1.3 74.9 - - - +
327A LYS* 1.3 56.1 + - - +
329A TYR* 4.2 0.2 - - - +
330A ASN* 2.6 50.1 + - - +
356A SER 4.6 1.3 - - - -
357A GLU* 3.6 28.5 - - - +
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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
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323A LYS 3.0 20.5 + - - +
324A LYS* 3.4 8.3 - - - +
326A CYS* 1.3 76.0 - - - +
328A PHE* 1.3 57.8 + - - +
330A ASN* 4.1 7.9 - - - +
331A GLN* 3.0 42.4 + - + +
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Residues in contact with PHE 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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187A GLU* 3.8 28.0 - - + -
263A GLY* 3.4 30.3 - - - -
267A ASN* 4.1 7.9 - - + -
296A PRO* 3.4 23.1 - - + -
297A GLY* 3.3 33.0 - - - +
324A LYS 2.7 16.2 + - - +
325A ALA* 2.8 9.9 + - - +
327A LYS* 1.3 70.9 - - - +
329A TYR* 1.3 68.9 + + - +
330A ASN 3.1 1.3 - - - -
331A GLN* 2.9 41.6 + - + +
332A ILE* 3.2 31.2 + - + +
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Residues in contact with TYR 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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262A THR* 4.3 4.3 - - - -
263A GLY* 3.7 14.0 + - - -
266A LEU* 3.9 15.0 - - + -
292A GLY* 5.2 0.7 + - - -
297A GLY* 2.9 40.3 + - - -
299A ILE* 4.0 16.1 - - + +
325A ALA* 2.8 30.6 + - + +
326A CYS 4.2 0.4 - - - +
328A PHE* 1.3 90.1 - + - +
330A ASN* 1.3 59.0 + - - +
332A ILE* 3.2 7.0 + - + +
333A ALA* 2.8 24.4 + - - +
357A GLU* 3.5 23.3 - - + +
358A MET* 3.6 46.0 - - + -
360A GLN* 5.6 0.7 - - + -
361A LEU* 3.4 24.9 - - + +
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Residues in contact with ASN 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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326A CYS* 2.6 41.3 + - - +
327A LYS* 4.0 7.2 - - - +
329A TYR* 1.3 75.0 - - - +
331A GLN* 1.3 67.1 + - - +
333A ALA* 3.6 5.6 - - - +
334A GLN* 2.9 43.1 + - + +
357A GLU 4.5 5.4 - - - +
360A GLN* 3.4 28.2 - - + +
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Residues in contact with GLN 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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187A GLU* 3.9 17.8 + - - +
327A LYS* 3.0 39.8 + - + +
328A PHE* 2.9 27.9 + - + +
330A ASN* 1.3 80.1 - - - +
332A ILE* 1.3 61.6 - - + +
334A GLN* 3.5 12.5 + - - +
335A ARG* 3.2 26.0 + - - +
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Residues in contact with ILE 332 (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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266A LEU* 4.0 14.4 - - + +
267A ASN* 3.7 27.4 - - + +
270A SER* 4.0 15.0 - - - +
328A PHE* 3.2 44.0 + - + +
329A TYR* 3.6 11.2 - - + +
330A ASN 3.1 0.2 - - - -
331A GLN* 1.3 75.8 - - + +
333A ALA* 1.3 65.9 + - - +
335A ARG* 3.0 23.0 + - - +
336A VAL* 2.9 30.7 + - + +
343A VAL* 5.7 1.1 - - + -
361A LEU* 3.6 17.3 - - + -
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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
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329A TYR 2.8 17.9 + - - +
330A ASN* 3.1 9.2 + - - +
332A ILE* 1.3 76.4 - - - +
334A GLN* 1.3 63.4 + - + +
336A VAL* 3.3 6.7 - - - +
337A ALA* 2.9 28.7 + - - +
360A GLN* 3.8 34.5 - - + +
361A LEU* 3.4 15.4 - - + +
364A SER* 4.2 6.3 - - - +
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Residues in contact with GLN 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 ASN* 2.9 32.4 + - + +
331A GLN* 3.8 10.5 - - - +
333A ALA* 1.3 75.7 - - + +
335A ARG* 1.3 56.9 + - - +
337A ALA* 4.0 4.1 - - - +
338A ALA* 2.9 32.7 + - - +
360A GLN* 6.4 1.1 - - + -
364A SER* 5.7 1.1 - - - +
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Residues in contact with ARG 335 (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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187A GLU* 5.2 5.9 + - - -
188A TYR 5.7 0.4 + - - -
267A ASN* 3.1 30.3 + - - +
270A SER* 2.8 48.1 + - - +
271A LEU* 3.4 22.8 - - - +
274A GLN* 3.8 15.3 + - - +
331A GLN* 3.2 15.0 + - - +
332A ILE* 3.0 22.2 + - - +
334A GLN* 1.3 76.4 - - - +
336A VAL* 1.3 56.6 + - - +
338A ALA* 3.2 3.5 + - - -
339A ASN* 2.7 57.8 + - - +
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Residues in contact with VAL 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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270A SER* 3.6 29.6 - - - +
284A ILE* 4.7 3.4 - - + -
332A ILE* 2.9 22.9 + - + +
333A ALA* 3.3 17.5 - - - +
335A ARG* 1.3 75.3 - - - +
337A ALA* 1.3 55.6 + - - +
339A ASN* 4.4 3.1 - - - -
340A GLY 2.7 13.5 + - - -
341A HIS* 2.6 52.3 + - + +
343A VAL* 3.8 25.8 - - + -
361A LEU* 4.8 1.6 - - + +
365A THR* 3.7 17.3 - - + -
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Residues in contact with ALA 337 (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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333A ALA 2.9 19.5 + - - +
334A GLN* 4.0 4.3 - - - +
336A VAL* 1.3 78.1 - - - +
338A ALA* 1.3 62.0 + - - +
340A GLY* 3.2 11.0 + - - -
364A SER* 3.9 14.6 - - - +
365A THR* 3.9 11.7 - - + -
422A SER* 3.6 25.6 - - - +
446A LYS* 3.1 21.9 - - - +
448A ALA* 5.8 0.8 - - - +
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Residues in contact with ALA 338 (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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278A LYS* 5.3 1.0 - - - -
279A ASN* 3.6 10.4 - - - +
334A GLN 2.9 21.0 + - - +
335A ARG* 3.7 4.0 - - - +
337A ALA* 1.3 76.7 - - - +
339A ASN* 1.3 67.9 + - - +
340A GLY* 3.1 1.1 + - - -
446A LYS* 4.4 14.4 - - - +
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Residues in contact with ASN 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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270A SER 4.7 0.9 - - - +
274A GLN* 3.2 39.0 - - - +
278A LYS* 3.1 37.0 - - + +
279A ASN* 2.7 35.9 + - - -
335A ARG* 2.7 33.4 + - - +
336A VAL* 4.0 3.3 - - - +
338A ALA* 1.3 78.3 - - - +
340A GLY* 1.3 61.6 + - - +
341A HIS* 3.8 18.9 + - + +
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Residues in contact with GLY 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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279A ASN* 5.0 3.2 - - - -
280A ILE 4.1 9.2 + - - +
281A PRO* 4.5 5.2 - - - +
282A ALA 4.5 0.2 + - - -
336A VAL 2.7 8.2 + - - -
337A ALA 3.2 8.5 + - - -
338A ALA 3.1 4.4 - - - -
339A ASN* 1.3 81.6 - - - +
341A HIS* 1.3 64.3 + - - -
401A ASN* 5.9 6.7 + - - +
446A LYS* 5.7 1.8 - - - -
448A ALA* 4.0 18.0 - - - +
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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