Contacts of the helix formed by residues 249 - 260 (chain A) in PDB entry 4J15
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A GLN* 1.3 79.6 - - - +
250A PRO* 1.3 81.8 - - - +
251A GLN* 2.4 20.9 + - - -
252A LEU* 2.6 16.6 + - - +
253A TYR* 4.0 2.7 + - - -
271A VAL* 5.0 4.9 - - - +
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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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220A THR* 4.2 18.5 - - - +
249A SER* 1.3 96.7 - - - +
251A GLN* 1.3 62.1 + - + +
253A TYR* 3.3 11.8 + - + +
254A LYS* 3.3 23.8 + - - +
267A SER* 4.7 7.9 - - - +
270A PRO 5.5 1.1 - - - +
271A VAL* 4.0 33.2 - - + -
290A ASP* 3.8 22.7 - - - +
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Residues in contact with GLN 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 SER* 2.4 10.4 + - - +
250A PRO* 1.3 75.6 - - + +
252A LEU* 1.3 64.1 + - - +
254A LYS* 3.6 25.2 - - - +
255A GLN* 3.0 59.2 + - - +
290A ASP* 5.6 0.4 - - - +
292A GLU* 3.7 1.6 + - - -
402A TYR* 3.4 33.3 + - - -
431A ARG* 3.2 36.4 - - - +
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Residues in contact with LEU 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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248A GLN* 3.4 39.7 - - + +
249A SER 2.6 18.7 + - - +
251A GLN* 1.3 73.4 - - - +
253A TYR* 1.3 71.6 + - + +
255A GLN* 3.7 4.6 - - - +
256A MET* 3.0 54.4 + - + +
455A TYR* 4.4 35.6 - - + -
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Residues in contact with TYR 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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218A ILE* 4.4 0.9 - - + -
220A THR* 3.7 27.8 - - + -
221A PRO* 3.6 36.5 + - + +
223A ILE* 6.0 2.1 - - - +
248A GLN* 3.8 42.8 - - + +
249A SER 4.1 10.5 - - - -
250A PRO* 3.3 3.8 + - + +
251A GLN 3.2 0.2 - - - -
252A LEU* 1.3 87.2 - - + +
254A LYS* 1.3 64.9 + - - +
256A MET* 3.3 8.3 + - - +
257A CYS* 3.0 28.0 + - - -
492B PHE* 3.5 42.5 - + + -
494B ARG* 5.2 6.6 + - - -
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Residues in contact with LYS 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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218A ILE* 3.9 22.4 - - + +
220A THR* 5.2 0.4 - - + -
250A PRO 3.3 10.4 + - - +
251A GLN* 3.6 30.2 - - - +
253A TYR* 1.3 76.4 - - - +
255A GLN* 1.3 58.6 + - - +
257A CYS* 3.2 4.2 + - - +
258A ILE* 3.0 32.3 + - - +
265A VAL* 4.1 7.1 - - + +
267A SER* 4.8 7.6 - - - +
290A ASP* 3.2 46.4 + - + +
291A ILE 3.1 15.1 + - - -
292A GLU* 3.0 42.5 + - + +
431A ARG* 4.0 4.9 - - - +
469A GLY* 4.1 2.6 - - - +
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Residues in contact with GLN 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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251A GLN* 3.0 46.2 + - - +
252A LEU 3.7 3.8 - - - +
254A LYS* 1.3 74.0 - - - +
256A MET* 1.3 61.5 + - - +
258A ILE* 3.2 8.2 + - - +
259A CYS* 2.8 34.2 + - - -
292A GLU* 4.4 3.6 - - - -
402A TYR* 5.1 0.5 - - - -
431A ARG* 3.3 18.9 - - - +
432A ILE 4.9 0.8 + - - -
455A TYR* 2.6 33.8 + - + -
458A SER* 5.8 0.4 - - - -
459A PHE* 3.4 24.2 - - + -
466A HIS* 2.8 34.0 + - + +
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Residues in contact with MET 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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252A LEU* 3.0 39.8 + - + +
253A TYR* 3.4 13.0 - - - +
255A GLN* 1.3 75.7 - - - +
257A CYS* 1.3 56.0 + - - +
259A CYS* 3.0 8.5 + - - +
260A ALA* 2.8 28.4 + - - +
455A TYR* 6.2 1.6 - - + -
458A SER* 4.6 11.9 + - - +
183B ARG* 3.8 19.5 - - + -
184B VAL* 3.7 31.2 - - + +
187B LEU* 5.5 1.8 - - + -
492B PHE* 3.5 33.2 - - + -
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Residues in contact with CYS 257 (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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218A ILE* 3.7 19.3 - - - -
253A TYR 3.0 18.9 + - - -
254A LYS* 3.2 8.3 + - - +
256A MET* 1.3 71.8 - - - +
258A ILE* 1.3 61.5 + - - +
260A ALA* 3.0 14.1 + - - -
261A ASP 3.2 0.3 + - - -
262A PHE* 2.9 46.6 + - + +
265A VAL* 4.2 9.6 - - + -
187B LEU* 5.4 1.3 - - - -
491B MET* 3.5 35.0 - - - -
492B PHE* 4.0 7.6 - - - -
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Residues in contact with ILE 258 (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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254A LYS 3.0 17.8 + - - +
255A GLN* 3.5 8.5 - - - +
257A CYS* 1.3 75.3 - - - +
259A CYS* 1.3 62.6 + - - +
260A ALA 3.0 1.5 + - - -
261A ASP* 3.2 12.8 + - - +
262A PHE 4.6 1.8 - - - +
263A GLU* 3.3 37.3 + - - +
265A VAL* 4.5 5.6 - - + -
292A GLU* 3.7 30.7 - - + +
293A MET 3.9 1.3 - - - +
294A ALA* 3.7 11.7 - - + +
464A PRO* 3.8 28.0 - - + +
466A HIS* 3.6 35.2 - - + +
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Residues in contact with CYS 259 (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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255A GLN 2.8 22.0 + - - +
256A MET 3.4 9.0 - - - +
258A ILE* 1.3 73.8 - - - +
260A ALA* 1.3 55.8 + - - +
261A ASP 3.4 1.3 - - - -
458A SER* 3.3 31.2 - - - +
459A PHE* 3.4 34.1 - - - -
463A ALA* 3.8 12.8 - - + -
464A PRO* 4.7 3.1 - - - -
466A HIS* 5.0 2.7 - - - -
65B ARG* 3.3 11.2 + - - +
184B VAL* 3.5 10.0 - - + +
188B ARG* 3.0 30.8 + - - +
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Residues in contact with ALA 260 (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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256A MET 2.8 14.9 + - - +
257A CYS* 3.0 12.8 + - - +
259A CYS* 1.3 77.1 - - - +
261A ASP* 1.3 63.5 + - - +
262A PHE* 3.9 2.4 - - + -
184B VAL* 3.4 24.9 - - - +
187B LEU* 3.5 24.6 - - + +
188B ARG* 3.7 8.5 - - + +
193B GLN* 2.9 23.0 + - - -
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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