Contacts of the helix formed by residues 321 - 335 (chain A) in PDB entry 2Y01
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 PRO 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ASP 4.6 2.6 - - - +
319A LEU 4.4 3.1 - - - +
320A VAL* 1.4 92.5 - - + +
322A ASP* 1.3 68.8 + - - +
323A TRP* 3.7 31.6 - - + +
324A LEU* 3.2 27.5 + - + +
325A PHE* 3.4 7.4 + - - +
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Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A VAL 3.6 2.5 + - - -
321A PRO* 1.3 71.9 - - - +
323A TRP* 1.3 65.2 + - - +
325A PHE* 2.9 28.3 + - - +
326A VAL* 3.1 27.5 + - - +
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Residues in contact with TRP 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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321A PRO* 3.7 26.7 - - + +
322A ASP* 1.3 79.3 + - - +
324A LEU* 1.3 93.6 + - + +
326A VAL* 3.7 8.6 + - - +
327A ALA* 3.1 33.4 + - + +
504A 2CV 6.5 0.7 - - - -
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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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320A VAL* 4.8 9.9 - - + -
321A PRO* 3.2 21.5 + - + +
322A ASP 3.1 0.8 - - - -
323A TRP* 1.3 114.7 - - + +
325A PHE* 1.3 60.0 + - - +
327A ALA* 3.4 6.2 + - + +
328A PHE* 2.9 74.0 + - + -
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Residues in contact with PHE 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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306A PHE* 3.3 45.2 - + - -
309A VAL* 3.3 32.5 - - + -
310A ASN* 3.9 20.6 - - - -
313A ASN* 3.8 20.6 - - - +
320A VAL* 4.9 3.0 - - + +
321A PRO 3.4 7.3 + - - +
322A ASP* 2.9 22.2 + - - +
324A LEU* 1.3 78.5 - - - +
326A VAL* 1.3 66.0 + - + +
328A PHE* 3.4 7.7 + - + +
329A ASN* 3.3 17.8 + - - +
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Residues in contact with VAL 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 ASP* 3.1 33.3 + - - +
323A TRP* 3.8 8.1 - - - +
325A PHE* 1.3 79.5 - - + +
327A ALA* 1.3 58.8 + - - +
329A ASN* 2.9 24.5 + - - +
330A TRP* 3.2 13.2 + - + -
504A 2CV 3.5 39.5 - - + -
601A Y00 3.7 28.9 - - + +
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Residues in contact with ALA 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 TRP* 3.1 22.8 + - + +
324A LEU* 3.5 16.2 - - + +
325A PHE 3.3 0.2 - - - -
326A VAL* 1.3 77.9 - - - +
328A PHE* 1.3 53.3 + - + +
330A TRP* 3.0 12.6 + - - +
331A LEU* 2.7 33.1 + - - +
504A 2CV 3.9 22.3 + - + +
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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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302A CYS 4.1 2.6 - - - +
305A PRO* 3.8 29.4 - - + -
306A PHE* 3.8 23.8 - - - +
309A VAL* 3.7 31.4 - - + -
320A VAL* 5.6 0.2 - - + -
324A LEU* 2.9 57.9 + - + +
325A PHE* 3.5 6.7 - - - +
326A VAL 3.2 0.2 - - - -
327A ALA* 1.3 76.8 - - + +
329A ASN* 1.3 63.9 + - - +
331A LEU* 3.3 21.5 + - + +
332A GLY* 3.1 17.7 + - - -
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Residues in contact with ASN 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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121A ASP* 4.1 3.2 + - - -
303A TRP* 3.6 19.8 - - - -
306A PHE* 3.6 23.8 - - + -
325A PHE 3.3 5.2 + - - +
326A VAL* 2.9 13.7 + - - +
328A PHE* 1.3 77.9 - - - +
330A TRP* 1.3 60.5 + - + +
332A GLY* 3.3 2.1 + - - -
333A TYR* 3.2 40.7 + - - -
601A Y00 3.1 49.0 + - + +
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Residues in contact with TRP 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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48A MET* 3.4 39.0 - - + -
51A VAL* 5.6 3.6 - - + -
95A VAL* 4.3 11.9 - - + -
98A GLY* 4.0 10.5 - - - -
99A ALA 3.9 11.4 - - - -
102A VAL* 3.6 22.6 - - + +
326A VAL* 3.2 20.9 + - + -
327A ALA* 3.0 9.3 + - - +
329A ASN* 1.3 75.4 - - - +
331A LEU* 1.3 64.3 + - - +
332A GLY 3.2 0.4 - - - -
333A TYR* 3.3 35.0 + + + +
334A ALA* 3.0 21.3 + - - +
504A 2CV 3.9 64.2 - - + +
601A Y00 3.1 28.8 - + - -
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Residues in contact with LEU 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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301A LEU 4.0 14.4 - - - +
302A CYS* 3.6 34.8 - - - +
305A PRO* 4.6 4.7 - - + -
327A ALA 2.7 16.2 + - - +
328A PHE* 3.5 32.3 - - + +
330A TRP* 1.3 73.4 - - - +
332A GLY* 1.3 61.1 + - - +
334A ALA* 3.1 22.1 + - + +
335A ASN 3.4 4.5 + - - -
338A MET* 4.8 0.9 - - + -
504A 2CV 4.3 29.3 + - - +
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Residues in contact with GLY 332 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A CYS* 3.5 8.2 + - - -
303A TRP* 3.3 45.1 + - - -
328A PHE 3.1 9.9 + - - -
329A ASN 3.3 4.7 + - - -
330A TRP 3.2 0.2 - - - -
331A LEU* 1.3 72.3 - - - +
333A TYR* 1.3 65.0 + - - +
335A ASN* 3.1 19.9 + - - +
336A SER* 4.3 2.1 + - - -
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Residues in contact with TYR 333 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A VAL* 6.1 1.3 - - + -
55A ILE* 4.1 7.9 - - - +
90A VAL* 4.1 10.4 - - + +
94A VAL* 3.6 26.7 - - + +
95A VAL* 3.9 20.9 - - + -
98A GLY* 5.6 0.4 - - - -
117A TRP* 3.9 8.3 - + - -
121A ASP* 2.7 41.1 + - - -
303A TRP* 4.2 6.7 - + - -
329A ASN* 3.2 20.6 + - - -
330A TRP* 3.3 51.5 + + + +
332A GLY* 1.3 75.6 - - - +
334A ALA* 1.3 62.1 + - - +
336A SER* 3.1 24.0 + - - -
601A Y00 3.4 24.2 - + - +
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Residues in contact with ALA 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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51A VAL* 5.8 5.4 - - + -
55A ILE* 5.5 2.7 - - - -
330A TRP 3.0 12.2 + - - +
331A LEU* 3.1 15.9 + - + +
333A TYR* 1.3 77.5 - - - +
335A ASN* 1.3 60.5 + - - +
337A ALA* 3.1 23.8 + - - +
338A MET* 3.6 15.2 - - + +
504A 2CV 3.9 38.8 + - - +
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Residues in contact with ASN 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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87A ASP* 4.6 10.5 + - - -
128A SER* 5.7 0.4 + - - -
295A ILE 5.0 0.2 - - - +
298A VAL* 3.8 12.3 - - - +
299A PHE* 3.3 55.5 + - - +
302A CYS* 3.7 16.7 - - + -
303A TRP* 4.5 3.6 - - - +
331A LEU 3.4 2.4 + - - -
332A GLY 3.1 13.8 + - - +
334A ALA* 1.3 79.0 - - - +
336A SER* 1.3 58.4 + - - +
337A ALA 3.0 6.1 + - - -
338A MET* 3.0 24.7 + - - +
339A ASN* 4.0 18.6 + - - +
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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