Contacts of the helix formed by residues 320 - 332 (chain A) in PDB entry 2BP1
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 SER 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A MET* 3.9 12.5 - - - -
318A MET* 3.4 10.8 - - - +
319A SER* 1.3 83.3 + - - +
321A LEU* 1.3 58.7 + - - +
322A GLU* 3.6 8.0 + - - +
323A GLN* 3.3 28.9 + - - +
324A LEU 3.1 20.8 + - - -
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Residues in contact with LEU 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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52A MET* 4.0 12.3 - - + +
56A ALA* 5.0 6.5 - - + +
59A ALA* 3.7 44.9 - - + +
60A ALA* 3.8 9.4 - - - +
63A ALA* 4.2 8.7 - - + -
320A SER* 1.3 72.4 - - - +
322A GLU* 1.3 60.2 + - - +
324A LEU* 3.7 7.4 - - + +
325A GLU* 3.0 52.9 + - + +
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Residues in contact with GLU 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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320A SER* 3.3 7.4 + - - +
321A LEU* 1.3 74.7 - - - +
323A GLN* 1.3 66.7 + - - +
325A GLU* 3.2 11.3 + - - +
326A GLN* 2.9 32.2 + - - +
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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
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237A LYS* 3.9 2.8 - - - +
318A MET* 3.3 4.8 - - + -
319A SER* 2.6 37.4 + - - -
320A SER* 3.3 18.3 + - - +
322A GLU* 1.3 78.9 - - - +
324A LEU* 1.3 61.5 + - - +
326A GLN* 3.4 4.8 + - - +
327A ASN* 3.0 30.7 + - - +
1361A NDP 2.8 80.5 + - + +
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Residues in contact with LEU 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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43A LEU* 3.7 27.6 - - + -
60A ALA* 3.5 45.1 - - + +
63A ALA* 4.4 5.6 - - + -
64A PHE* 4.7 1.3 - - + +
316A LEU* 4.6 13.0 - - + -
317A GLY 5.5 0.9 - - - +
318A MET* 3.9 18.5 - - + +
320A SER 3.1 11.2 + - - +
321A LEU* 3.7 10.5 - - + +
322A GLU 3.3 0.2 - - - -
323A GLN* 1.3 79.8 - - - +
325A GLU* 1.3 56.6 + - - +
327A ASN* 3.2 5.0 + - + -
328A LEU* 2.8 54.9 + - + +
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Residues in contact with GLU 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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63A ALA* 4.5 15.2 - - + +
67A ARG* 4.5 5.2 + - - +
321A LEU* 3.0 50.2 + - + +
322A GLU* 3.7 10.0 - - - +
324A LEU* 1.3 72.5 - - - +
326A GLN* 1.3 65.2 + - - +
328A LEU* 3.5 8.8 + - + +
329A ALA* 3.1 23.2 + - - +
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Residues in contact with GLN 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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293A THR* 4.5 12.6 + - + +
322A GLU* 2.9 23.8 + - - +
323A GLN* 3.4 5.2 - - - +
325A GLU* 1.3 76.7 - - - +
327A ASN* 1.3 61.7 + - - +
329A ALA* 3.3 9.7 + - - +
330A ALA* 3.2 19.6 + - - +
1361A NDP 2.8 34.8 + - - +
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Residues in contact with ASN 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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229A LEU* 4.1 6.4 - - - +
293A THR* 3.7 12.6 - - - +
297A LEU* 3.8 19.7 - - + +
316A LEU* 4.4 14.8 - - + +
317A GLY 3.0 30.1 + - - +
323A GLN 3.0 17.2 + - - +
324A LEU* 3.2 6.2 + - + +
326A GLN* 1.3 77.0 - - - +
328A LEU* 1.3 61.6 + - - +
330A ALA* 3.2 5.6 + - - +
331A THR* 3.1 26.1 + - - +
1361A NDP 2.9 39.4 + - - -
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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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63A ALA* 3.9 32.1 - - + +
64A PHE* 4.1 8.3 - - + -
67A ARG* 3.8 30.4 + - + +
69A HIS* 4.1 28.7 - - + +
316A LEU* 3.7 23.8 - - + -
324A LEU* 2.8 42.0 + - + +
325A GLU* 3.8 7.9 - - + +
326A GLN 3.4 0.2 - - - -
327A ASN* 1.3 73.2 - - - +
329A ALA* 1.3 59.3 + - - +
331A THR* 2.6 24.0 + - - +
332A GLU* 3.5 3.1 + - - +
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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
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67A ARG* 3.9 15.5 - - - +
325A GLU 3.1 13.5 + - - +
326A GLN* 3.4 11.9 - - - +
327A ASN 3.2 0.2 - - - -
328A LEU* 1.3 77.0 - - - +
330A ALA* 1.3 61.9 + - - +
332A GLU* 3.1 15.2 + - - +
333A GLU* 3.4 22.8 + - - +
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Residues in contact with ALA 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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293A THR* 5.9 0.4 - - + -
294A SER* 3.9 28.9 - - - +
297A LEU* 3.8 22.4 - - + -
298A ARG* 3.5 12.7 - - - +
326A GLN 3.2 7.4 + - - +
327A ASN 3.2 10.1 + - - +
329A ALA* 1.3 79.6 - - - +
331A THR* 1.3 62.6 + - - +
333A GLU* 3.0 29.1 + - - +
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Residues in contact with THR 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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41A SER* 4.2 6.3 - - - +
69A HIS* 4.6 11.1 + - - -
297A LEU* 5.2 1.6 - - + -
301A TYR* 3.3 58.1 - - + +
302A HIS* 4.8 3.8 + - - -
316A LEU* 3.9 14.4 - - + -
327A ASN 3.1 14.8 + - - +
328A LEU* 2.6 25.5 + - + +
330A ALA* 1.3 77.3 - - - +
332A GLU* 1.3 63.2 + - - +
333A GLU 3.6 5.2 + - - +
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Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG* 3.4 30.3 - - + +
69A HIS* 6.1 2.0 - - - +
328A LEU 3.8 4.3 - - - +
329A ALA* 3.1 9.9 + - - +
331A THR* 1.3 81.9 + - - +
333A GLU* 1.3 63.7 + - - +
334A GLY 4.1 0.2 + - - -
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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