Contacts of the helix formed by residues 310 - 326 (chain A) in PDB entry 2DH2
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 THR 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A SER* 1.3 81.2 - - - +
311A GLY* 1.3 58.8 + - - +
312A GLU* 3.7 10.8 + - - +
313A HIS* 3.2 22.3 + - - +
314A THR* 3.1 26.5 + - - -
447A PRO 5.4 2.7 - - - -
448A GLY* 5.4 3.8 - - - -
468A PHE* 4.0 5.6 - - - -
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Residues in contact with GLY 311 (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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310A THR* 1.3 71.2 - - - +
312A GLU* 1.3 60.1 + - - +
315A LYS* 2.9 30.8 + - - +
448A GLY* 3.6 18.6 + - - -
449A LEU 3.8 9.9 - - - -
450A PHE* 3.7 5.4 - - - +
468A PHE* 3.4 33.2 - - - +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A THR* 3.4 8.2 - - - +
311A GLY* 1.3 76.5 - - - +
313A HIS* 1.3 58.2 + - - +
315A LYS* 3.5 18.8 + - - +
316A SER* 3.0 28.8 + - - -
445A ALA 4.5 4.0 + - - +
446A GLY 2.9 17.4 - - - +
447A PRO* 2.6 30.3 - - + +
449A LEU 3.3 13.4 - - - +
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Residues in contact with HIS 313 (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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306A ASP* 3.2 34.4 + - - -
309A SER* 3.0 28.7 + - - +
310A THR* 3.2 20.9 + - - +
312A GLU* 1.3 77.6 - - - +
314A THR* 1.3 59.5 + - - +
316A SER* 2.7 23.5 + - - -
317A LEU* 3.0 39.4 + - + +
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Residues in contact with THR 314 (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 LEU* 5.0 3.6 - - + -
307A SER* 3.7 21.0 - - - +
309A SER* 3.8 1.2 + - - -
310A THR 3.1 15.2 + - - -
311A GLY 4.0 2.9 - - - -
312A GLU 3.4 0.2 - - - -
313A HIS* 1.3 74.1 - - - +
315A LYS* 1.3 65.0 + - - +
317A LEU* 3.5 9.5 + - - +
318A VAL* 3.1 27.7 + - + +
352A TYR* 3.9 2.5 + - - +
355A MSE 3.6 36.8 - - + -
450A PHE* 4.1 4.3 - - + -
468A PHE* 3.7 27.4 - - + -
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Residues in contact with LYS 315 (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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311A GLY 2.9 18.7 + - - +
312A GLU* 3.5 21.3 + - - +
314A THR* 1.3 77.1 - - - +
316A SER* 1.3 62.0 + - - +
318A VAL* 3.4 1.4 + - - +
319A THR* 2.9 38.9 + - + +
442A ALA* 4.3 13.7 - - - -
443A PHE* 3.0 33.8 + - - +
444A SER* 3.8 10.3 + - - +
445A ALA 4.8 1.4 - - - +
449A LEU 5.1 5.2 - - - +
450A PHE* 3.5 37.2 - - + -
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Residues in contact with SER 316 (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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312A GLU 3.0 15.0 + - - -
313A HIS* 2.7 31.4 + - - -
315A LYS* 1.3 76.5 - - - +
317A LEU* 1.3 55.3 + - - +
319A THR* 3.5 6.5 - - - -
320A GLN* 2.8 50.9 + - - +
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Residues in contact with LEU 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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303A TYR* 2.6 63.6 + - + +
304A LEU* 4.2 10.1 - - + -
306A ASP* 3.5 26.5 - - - +
307A SER* 4.1 18.4 - - - -
313A HIS* 3.0 40.8 + - + +
314A THR* 3.7 5.2 - - - +
315A LYS 3.3 0.2 - - - -
316A SER* 1.3 77.1 + - - +
318A VAL* 1.3 62.1 + - - +
320A GLN* 4.5 9.4 - - - +
321A TYR* 3.1 10.4 + - - +
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.1 19.3 - - + -
314A THR* 3.1 25.5 + - + +
315A LYS 3.9 2.7 - - - +
317A LEU* 1.3 76.2 - - - +
319A THR* 1.3 58.5 + - - +
321A TYR* 3.3 3.8 + - - +
322A LEU* 3.0 39.9 + - + +
332A TRP* 3.8 18.6 - - + -
355A MSE 4.6 1.1 - - - -
359A LEU* 3.7 40.2 - - + -
440A PHE* 4.1 10.3 - - + -
450A PHE* 4.1 13.7 - - + -
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Residues in contact with THR 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 LYS* 2.9 29.2 + - + +
316A SER* 3.2 9.7 + - - -
318A VAL* 1.3 72.2 - - + +
320A GLN* 1.3 70.2 + - - +
321A TYR 3.2 1.1 - - - -
322A LEU* 4.5 6.1 - - - -
323A ASN* 2.9 40.3 + - - +
440A PHE* 4.2 13.7 - - + -
442A ALA* 4.2 25.4 - - + -
450A PHE* 5.3 0.4 - - + -
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Residues in contact with GLN 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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284A LEU* 4.2 17.9 - - + +
303A TYR* 3.7 12.6 - - - +
316A SER* 2.8 42.6 + - - +
317A LEU* 4.7 10.1 - - - +
319A THR* 1.3 74.4 + - - +
321A TYR* 1.3 62.0 + - - +
323A ASN* 4.0 6.2 - - - +
324A ALA* 3.1 24.6 + - - +
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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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284A LEU* 3.5 28.9 - - + -
287A ILE* 4.1 18.9 - - + +
288A LEU* 4.8 0.7 - - + -
291A LEU* 3.8 17.8 - - - +
299A LEU* 4.6 12.6 + - - +
301A SER* 6.1 0.4 - - - -
303A TYR* 3.7 24.0 + + + -
317A LEU 3.1 19.2 + - - +
318A VAL 3.5 5.4 - - - +
320A GLN* 1.3 77.0 - - - +
322A LEU* 1.3 60.2 + - - +
324A ALA* 3.3 2.3 + - - +
325A THR* 2.9 44.1 + - + +
330A CYS* 3.1 37.2 - - + +
331A SER 4.6 8.8 + - - -
332A TRP* 3.9 20.0 - + + -
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Residues in contact with LEU 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 VAL* 3.0 31.4 + - + +
319A THR* 3.9 3.8 - - - +
321A TYR* 1.3 75.3 - - - +
323A ASN* 1.3 66.3 + - - +
325A THR* 3.3 4.4 + - - +
326A GLY* 3.3 30.0 + - - +
328A ARG 5.7 3.6 - - - +
330A CYS* 4.4 13.9 - - + -
332A TRP* 3.9 19.7 - - + -
360A PRO* 4.0 25.4 - - + +
440A PHE* 3.7 36.8 - - + -
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Residues in contact with ASN 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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319A THR* 2.9 31.6 + - - +
320A GLN* 4.0 5.4 - - - +
322A LEU* 1.3 79.7 - - - +
324A ALA* 1.3 61.3 + - - +
325A THR 3.5 0.2 + - - -
326A GLY* 3.6 9.4 + - - -
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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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284A LEU* 4.9 4.3 - - + -
288A LEU* 3.8 35.8 - - + +
320A GLN 3.1 18.1 + - - +
321A TYR* 3.3 6.5 + - - +
323A ASN* 1.3 77.1 - - - +
325A THR* 1.3 60.7 + - - +
326A GLY 3.4 0.4 + - - -
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 4.0 19.3 - - + -
291A LEU* 4.1 20.2 - - + -
321A TYR* 2.9 31.6 + - + +
322A LEU* 3.3 9.4 + - - +
323A ASN 3.3 0.2 - - - -
324A ALA* 1.3 78.6 - - - +
326A GLY* 1.3 63.5 + - - +
327A ASN 3.5 0.5 + - - -
328A ARG* 3.2 39.5 + - - +
330A CYS* 3.6 16.0 - - - -
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Residues in contact with GLY 326 (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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322A LEU* 3.3 19.8 + - - +
323A ASN 3.6 6.9 + - - -
324A ALA 3.4 4.0 + - - -
325A THR* 1.3 80.1 + - - +
327A ASN* 1.3 65.4 + - - +
328A ARG 3.4 2.5 + - - +
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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
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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