Contacts of the helix formed by residues 249 - 256 (chain A) in PDB entry 3ZJU
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 ARG 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A THR* 3.1 5.8 + - - -
248A THR* 1.3 94.6 - - - +
250A PRO* 1.3 65.4 - - - +
251A ASP* 2.9 35.9 + - - +
252A THR* 2.9 33.9 + - - +
336A MET* 3.2 6.1 - - - +
341A HIS* 4.9 4.9 + - - +
360A ILE* 4.1 11.3 - - - +
376A THR 3.6 21.6 + - - -
377A GLU 4.3 2.0 + - - -
378A LYS* 3.8 47.4 - - - +
392A HIS* 3.8 2.4 + - - -
76B DJF 3.6 48.6 - - + -
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Residues in contact with PRO 250 (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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230A VAL* 3.6 36.8 - - + -
232A ILE* 4.9 4.3 - - + -
247A THR* 4.0 12.2 - - + +
248A THR* 3.5 2.0 - - - -
249A ARG* 1.3 88.6 - - - +
251A ASP* 1.3 56.2 + - - +
252A THR 3.0 0.2 - - - -
253A PHE* 2.7 36.5 + - + +
336A MET* 4.2 3.6 - - + -
396A PHE* 3.3 47.3 - - + +
399A ILE* 3.8 17.9 - - + +
400A ALA 5.0 1.3 - - - +
403A LEU* 5.4 0.4 - - + -
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Residues in contact with ASP 251 (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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249A ARG* 2.9 52.5 + - - -
250A PRO* 1.3 81.8 - - - +
252A THR* 1.3 59.8 + - - +
253A PHE 3.2 1.7 + - - -
254A MET* 5.1 0.7 + - - +
359A VAL* 5.3 0.2 - - - +
360A ILE* 3.8 7.1 - - - +
379A GLY 5.2 0.7 + - - +
381A LEU* 3.2 31.7 - - + +
384A SER* 5.1 1.2 + - - -
392A HIS* 3.5 26.0 + - + +
395A ALA* 4.0 10.5 - - + -
396A PHE* 3.8 24.6 - - - +
399A ILE* 4.0 10.3 - - - +
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Residues in contact with THR 252 (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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249A ARG* 2.9 37.8 + - + +
250A PRO 2.9 0.8 + - - -
251A ASP* 1.3 92.4 - - - +
253A PHE* 1.3 58.2 + - - +
254A MET 3.3 3.1 - - - -
255A GLY* 2.8 23.8 + - - -
336A MET* 3.6 1.5 - - - +
338A VAL* 3.4 37.1 - - + +
341A HIS* 4.5 6.1 - - + -
359A VAL* 4.1 10.3 - - - -
360A ILE* 3.8 15.9 - - + -
384A SER* 6.1 0.2 - - - -
76B DJF 3.7 5.2 - - + -
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Residues in contact with PHE 253 (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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232A ILE* 3.8 18.8 - - + -
234A PHE* 3.8 16.2 - + - -
250A PRO* 2.7 17.6 + - + +
251A ASP 3.2 3.0 + - - -
252A THR* 1.3 77.5 + - - +
254A MET* 1.3 58.0 + - - +
256A CYS* 3.0 30.8 + - + +
311A HIS* 3.1 35.3 + + - -
312A PRO* 3.6 39.9 - - + -
313A LEU* 4.2 15.3 - - + -
336A MET* 3.3 31.2 - - + -
399A ILE* 4.1 12.1 - - + +
403A LEU* 3.9 24.9 - - + -
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Residues in contact with MET 254 (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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251A ASP 5.1 0.4 + - - +
252A THR 3.2 1.0 + - - -
253A PHE* 1.3 77.0 - - - +
255A GLY* 1.3 57.8 + - - +
256A CYS 3.2 4.0 + - - +
311A HIS* 4.2 9.5 + - - -
313A LEU* 3.7 40.6 - - + +
314A THR* 3.3 26.5 - - - +
316A GLU* 5.0 5.4 - - - +
357A LYS* 3.2 25.0 + - - +
359A VAL* 3.7 2.5 - - - -
381A LEU* 5.8 0.2 - - + -
383A ASN 4.0 4.7 - - - +
384A SER* 3.5 54.5 + - - +
385A GLY* 5.1 2.0 - - - +
387A PHE* 4.5 8.3 - - + -
399A ILE* 5.0 4.5 - - + -
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Residues in contact with GLY 255 (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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252A THR 2.8 13.1 + - - -
254A MET* 1.3 75.3 - - - +
256A CYS* 1.3 61.9 + - - +
257A THR* 3.2 17.8 + - - +
338A VAL* 4.0 17.6 - - - +
339A PRO* 4.0 4.2 - - - +
357A LYS* 4.2 14.5 - - - +
359A VAL* 3.5 25.3 - - - +
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Residues in contact with CYS 256 (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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234A PHE* 4.6 0.7 - - - -
252A THR 3.9 0.8 + - - -
253A PHE* 3.0 30.0 + - + +
254A MET 3.2 1.7 - - - +
255A GLY* 1.3 76.1 - - - +
257A THR* 1.3 58.6 + - - +
258A TYR 3.8 6.7 - - - -
259A LEU* 3.8 7.4 - - - -
311A HIS* 3.9 13.9 - - + -
316A GLU* 3.8 16.6 - - - +
318A ILE* 3.6 25.6 - - - +
336A MET* 3.8 24.2 - - - -
337A ALA 3.3 9.4 - - - +
338A VAL* 4.0 9.6 - - + -
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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