Contacts of the helix formed by residues 317 - 323 (chain A) in PDB entry 2P2J
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 LEU 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ILE* 4.7 10.3 - - + -
146A ALA* 3.8 33.0 - - + +
149A MET* 3.5 39.3 - - + -
150A LEU* 5.7 1.6 - - + -
307A VAL* 3.9 10.5 - - + -
312A GLY 3.4 9.1 + - - +
313A HIS 3.8 5.4 - - - +
316A LEU* 1.3 102.5 - - + +
318A TYR* 1.3 73.6 + - + +
319A GLY 3.6 1.3 - - - -
320A PRO* 3.5 1.7 - - - +
321A LEU* 3.0 47.2 + - + +
327A THR* 5.1 1.8 - - + -
329A MET* 4.4 4.3 - - + -
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Residues in contact with TYR 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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77A LEU* 3.5 36.6 - - + -
81A CYS* 3.9 5.7 - - - -
149A MET* 3.4 35.8 + - + +
150A LEU* 3.8 21.3 - - + -
153A ALA* 4.4 3.3 - - + +
159A HIS* 2.9 30.5 + + - -
259A LEU* 4.6 1.3 - - + -
260A PHE* 4.5 12.6 - + - -
281A TYR* 3.6 27.4 - + + +
282A LEU* 4.0 16.3 - - + +
285A ALA* 5.0 0.4 - - + -
313A HIS* 2.8 28.2 + - + +
314A SER* 4.5 0.4 - - - +
317A LEU* 1.3 79.3 - - + +
319A GLY* 1.3 62.8 + - - +
322A ALA* 3.0 27.4 + - - +
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Residues in contact with GLY 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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285A ALA* 3.9 28.9 - - - +
286A ALA* 4.1 2.0 - - - -
289A PHE* 4.1 8.1 - - - -
314A SER 2.8 20.1 + - - -
318A TYR* 1.3 74.3 - - - +
320A PRO* 1.3 67.7 - - - +
322A ALA* 3.5 2.3 + - - +
323A CYS* 3.3 25.3 + - - +
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Residues in contact with PRO 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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289A PHE* 3.8 24.7 - - + -
301A TYR* 3.7 12.3 - - + -
314A SER 3.5 8.7 - - - +
315A TYR* 3.5 24.5 - - - +
316A LEU 3.5 10.8 - - - +
317A LEU 3.5 9.4 - - - +
319A GLY* 1.3 90.0 - - - +
321A LEU* 1.3 60.5 + - - +
323A CYS* 3.0 8.5 + - - -
325A ALA* 3.0 30.5 + - + +
327A THR* 3.8 22.7 - - + -
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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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81A CYS* 3.6 22.7 - - + +
85A HIS* 2.9 19.6 + - - -
94A ALA* 3.9 28.7 - - + +
95A ILE* 4.6 3.1 - - + -
110A TYR* 3.5 23.0 + - + +
113A LEU* 4.1 9.9 - - + -
150A LEU* 3.9 33.0 - - + -
317A LEU* 3.0 39.1 + - + +
320A PRO* 1.3 70.9 - - - +
322A ALA* 1.3 66.5 - - - +
323A CYS 3.0 1.6 - - - -
324A GLY* 3.0 7.4 + - - -
325A ALA 4.2 1.3 - - - +
327A THR* 4.0 13.2 - - + -
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Residues in contact with ALA 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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46A LEU* 4.5 5.8 - - + -
80A ASN 3.6 13.0 - - - +
81A CYS* 3.6 10.9 - - - -
84A ARG* 2.8 31.2 + - - +
85A HIS* 3.3 10.7 - - - -
282A LEU* 4.2 11.0 - - + -
286A ALA* 4.0 18.8 - - + -
318A TYR 3.0 19.1 + - - +
319A GLY 3.8 4.3 - - - +
321A LEU* 1.3 76.4 - - - +
323A CYS* 1.3 57.2 + - - +
324A GLY 3.3 0.2 - - - -
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Residues in contact with CYS 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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45A ILE* 4.5 6.5 - - - -
85A HIS* 4.2 2.2 - - - -
92A ARG* 5.2 0.5 + - - -
286A ALA* 3.4 34.8 - - - -
289A PHE* 3.9 20.9 - - + -
290A LYS* 4.0 19.3 - - + -
295A TYR* 3.9 18.3 - - + -
319A GLY 3.3 11.4 + - - +
320A PRO 3.0 9.7 + - - +
321A LEU 3.0 1.2 - - - -
322A ALA* 1.3 78.3 - - - +
324A GLY* 1.3 61.1 + - - +
325A ALA 3.3 0.6 + - - +
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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