Contacts of the helix formed by residues 245 - 256 (chain A) in PDB entry 5C6P
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 LYS 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A LYS* 5.4 8.4 - - - +
239A PRO* 5.0 17.0 - - - +
240A ASP* 4.1 22.2 + - + +
241A TRP 2.8 20.9 + - - +
242A ALA* 3.4 12.5 - - + +
244A PHE* 1.3 71.1 - - - +
246A GLN* 1.3 65.5 + - - +
248A TRP* 3.0 31.5 - - + +
249A LYS* 4.2 1.6 + - - +
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Residues in contact with GLN 246 (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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80A MET* 3.3 35.1 - - + +
84A LEU* 5.5 7.7 - - - +
96A THR* 5.5 5.6 - - - +
242A ALA* 3.9 5.3 - - + +
243A VAL* 3.6 39.0 + - - +
244A PHE 3.4 0.6 - - - +
245A LYS* 1.3 76.7 - - - +
247A ILE* 1.3 54.9 + - - +
248A TRP 2.6 17.0 + - - -
249A LYS* 3.4 11.4 + - - +
250A ILE* 3.7 7.7 + - - +
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Residues in contact with ILE 247 (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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73A ILE* 4.6 3.9 - - - +
74A MET* 6.0 0.2 - - - -
77A LEU* 3.5 33.7 - - + -
80A MET* 4.3 11.2 - - - -
96A THR* 5.1 5.8 - - + +
100A GLY* 3.9 28.0 - - - +
103A PHE* 3.6 28.4 - - + -
243A VAL 3.5 21.3 - - - +
244A PHE* 3.4 24.9 - - + +
246A GLN* 1.3 72.8 - - + +
248A TRP* 1.3 56.1 + - - +
250A ILE* 3.3 14.6 - - + -
251A GLY* 3.1 18.9 + - - -
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Residues in contact with TRP 248 (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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73A ILE* 6.3 0.7 - - + -
103A PHE* 5.1 13.8 - + - -
244A PHE 3.5 9.7 + - - -
245A LYS* 3.0 26.2 + - + +
246A GLN 2.6 8.3 + - - -
247A ILE* 1.3 71.4 - - - +
249A LYS* 1.3 57.6 + - + +
250A ILE 3.1 3.6 - - - -
251A GLY 3.1 1.4 + - - -
252A ALA* 2.9 70.3 + - + +
256A LEU* 5.4 2.7 - - + -
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Residues in contact with LYS 249 (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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245A LYS 4.2 1.5 + - - +
246A GLN 3.4 5.4 + - - +
248A TRP* 1.3 80.0 - - + +
250A ILE* 1.3 59.8 + - - +
252A ALA* 5.0 0.2 - - - -
253A PRO* 3.1 24.1 - - + +
392A VAL* 4.8 14.4 - - + +
394A LYS* 3.9 5.7 - - - +
395A VAL* 3.6 39.6 + - + +
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Residues in contact with ILE 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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76A ALA* 2.9 46.4 - - + +
79A PRO* 4.7 8.1 - - + -
80A MET* 3.6 27.4 - - + -
246A GLN 3.7 5.3 + - - +
247A ILE* 3.3 39.0 - - + +
249A LYS* 1.3 79.6 - - - +
251A GLY* 1.3 64.2 + - - +
253A PRO* 3.2 0.3 - - - +
388A ARG* 6.4 0.7 - - + -
391A LYS 4.9 9.9 - - - +
392A VAL* 5.0 12.6 - - + +
394A LYS* 2.5 45.0 + - + +
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Residues in contact with GLY 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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73A ILE* 3.1 40.4 - - - -
76A ALA* 3.3 1.6 - - - -
247A ILE 3.1 14.9 + - - -
248A TRP 3.1 3.6 + - - -
250A ILE* 1.3 76.6 - - - +
252A ALA* 1.3 64.0 + - - +
254A ILE* 2.6 28.4 + - - +
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Residues in contact with ALA 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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73A ILE* 4.0 12.4 - - - +
248A TRP* 2.9 50.0 + - + +
249A LYS* 5.0 0.4 - - - -
251A GLY* 1.3 67.6 - - - -
253A PRO* 1.3 70.8 - - + +
254A ILE 2.9 6.6 + - - -
255A GLY* 3.0 5.4 + - - -
256A LEU* 2.9 38.7 + - + +
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Residues in contact with PRO 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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249A LYS* 3.1 33.4 - - + +
250A ILE 3.2 11.0 - - - +
252A ALA* 1.3 96.3 - - + +
254A ILE* 1.3 56.0 + - - -
256A LEU* 4.1 9.9 - - + -
257A SER* 2.9 29.0 + - - -
394A LYS* 3.2 30.8 - - + +
395A VAL* 4.5 5.8 - - - +
398A PHE* 3.5 19.0 + - + -
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Residues in contact with ILE 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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72A GLY* 2.8 30.5 - - - +
73A ILE* 3.9 0.2 - - - -
76A ALA 4.7 0.2 - - - +
250A ILE 3.5 0.9 - - - +
251A GLY* 2.6 26.7 + - - +
253A PRO* 1.3 78.8 - - - +
255A GLY* 1.3 52.4 + - - +
256A LEU 3.4 0.2 - - - -
257A SER* 4.0 10.1 - - - -
258A TYR* 2.6 61.4 + - + +
384A SER* 5.4 2.7 - - - +
385A TYR* 3.5 34.5 - - + +
388A ARG* 3.8 17.9 - - - +
394A LYS* 3.0 31.5 - - + +
397A MET* 6.3 0.7 - - + -
400A HIS* 5.9 1.8 - - + -
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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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69A THR* 3.6 24.9 + - - -
73A ILE* 3.5 22.8 - - - +
251A GLY 3.4 1.2 + - - -
252A ALA 3.0 3.8 + - - -
254A ILE* 1.3 83.7 - - - +
256A LEU* 1.3 54.8 + - - +
257A SER 3.1 1.3 - - - -
258A TYR* 2.9 7.0 + - - +
259A PHE* 2.7 29.6 + - - +
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Residues in contact with LEU 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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69A THR* 5.2 3.1 - - - +
73A ILE* 5.1 5.2 - - + -
248A TRP* 5.4 2.2 - - + -
252A ALA* 2.9 40.9 + - + +
253A PRO* 4.1 4.9 - - + -
255A GLY* 1.3 78.2 - - - +
257A SER* 1.3 57.9 - - - +
259A PHE* 3.1 36.4 - - + +
260A LEU 4.3 0.2 + - - -
398A PHE* 3.7 37.3 - - + +
401A ALA* 5.4 1.9 - - - +
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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