Contacts of the helix formed by residues 245 - 255 (chain A) in PDB entry 5MKE
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 ASN 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A SER* 3.8 12.9 + - - +
244A SER* 1.3 81.0 + - - +
246A VAL* 1.3 89.8 + - - +
247A TYR 3.1 0.7 - - - -
248A TYR* 3.0 19.2 + - + +
249A TYR* 2.9 17.3 + - - +
433A ILE* 4.7 11.4 - - - +
347B VAL* 5.1 13.3 - - - +
383B ILE* 5.6 10.3 - - + -
446B PRO* 4.9 13.5 - - + +
447B ALA* 4.8 5.7 - - - +
448B THR* 3.1 32.5 + - + +
628B THR* 6.2 0.2 - - - -
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Residues in contact with VAL 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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241A MET 5.1 0.2 - - - +
242A MET* 4.1 20.9 - - + -
243A SER 3.1 28.5 - - - +
244A SER 2.8 1.0 + - - -
245A ASN* 1.3 88.8 + - - +
247A TYR* 1.3 62.1 + - - +
249A TYR* 3.0 20.9 + - + +
250A THR* 3.0 14.0 + - + +
433A ILE* 4.3 18.2 - - + -
435A LEU* 4.3 19.5 - - + -
459A PRO* 4.7 18.2 - - + -
620B GLY* 4.3 6.7 - - - +
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Residues in contact with TYR 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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244A SER 3.3 3.3 + - - +
246A VAL* 1.3 73.6 - - - +
248A TYR* 1.3 102.8 + + - +
250A THR* 2.2 30.7 + - - -
251A ARG* 3.0 19.2 + - - +
620B GLY* 3.3 12.9 + - - +
621B THR 3.9 14.4 - - - -
623B VAL* 3.0 28.9 - - + -
624B ASP* 2.4 36.4 + - - +
625B ASP 4.0 1.1 + - - -
626B PHE 3.3 24.7 - - - -
627B SER* 3.1 36.8 - - - +
628B THR* 3.9 4.3 - - + -
631B GLU* 5.5 3.1 - - - -
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Residues in contact with TYR 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASN* 3.0 21.0 + - + +
247A TYR* 1.3 93.5 - + - +
249A TYR* 1.3 55.0 + - - +
250A THR 2.6 13.7 + - - -
251A ARG* 2.7 52.3 + - + -
252A MET* 2.8 27.9 + - + -
382B ILE* 4.5 9.0 - - + +
383B ILE* 5.3 11.0 - - + -
446B PRO* 5.2 11.9 - - + -
448B THR* 5.0 0.9 - - - +
451B VAL 6.3 0.7 - - - -
452B ILE* 3.1 44.9 - - + +
628B THR* 3.4 29.7 - - + +
631B GLU* 5.3 3.1 + - - -
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Residues in contact with TYR 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 ASN 2.9 6.5 + - - -
246A VAL* 3.0 24.0 + - + +
248A TYR* 1.3 73.9 - - - +
250A THR* 1.3 56.8 + - + +
252A MET* 3.5 12.9 - - + -
253A MET* 3.1 48.5 - - + +
313A ASN* 3.1 23.7 + - - -
429A TYR* 3.8 1.9 + - - -
430A ASN* 3.1 52.1 + - + +
433A ILE* 5.4 1.1 - - + -
435A LEU* 3.8 21.9 + - + -
437A CYS* 4.4 17.1 - - + +
459A PRO* 5.4 3.1 - - + -
448B THR* 3.5 32.1 - - + -
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Residues in contact with THR 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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246A VAL* 3.0 8.9 + - + +
247A TYR* 2.2 24.4 + - - -
248A TYR 2.6 5.3 + - - -
249A TYR* 1.3 73.4 - - + +
251A ARG* 1.3 59.9 + - - +
253A MET* 2.8 6.8 + - - +
254A SER* 2.7 35.0 + - - -
457A PHE* 5.6 4.8 - - + -
459A PRO* 5.2 15.3 - - + -
620B GLY 3.2 24.2 - - - +
621B THR* 3.6 5.1 + - - -
622B GLN* 3.0 35.6 - - - +
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Residues in contact with ARG 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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247A TYR* 3.0 28.0 - - + +
248A TYR* 2.7 49.4 + - - +
250A THR* 1.3 83.8 + - - +
252A MET* 1.3 67.5 + - - +
254A SER* 2.5 39.1 + - - +
255A GLN* 3.0 34.3 + - + +
451B VAL 5.7 2.4 + - - -
452B ILE* 5.2 4.0 - - - +
622B GLN* 4.0 13.7 - - + +
624B ASP* 2.8 36.4 + - - +
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Residues in contact with MET 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 TYR* 2.8 40.1 + - + +
249A TYR* 3.5 20.9 - - + -
251A ARG* 1.3 80.6 - - + +
253A MET* 1.3 62.2 + - + +
255A GLN* 5.5 2.0 - - - -
256A LEU* 3.3 30.3 - - - +
313A ASN* 5.1 1.8 - - - +
446B PRO* 5.6 1.1 - - - -
448B THR* 2.6 46.4 - - - +
449B GLY* 3.3 4.7 - - - -
450B GLY* 3.1 42.7 - - - +
451B VAL 4.8 4.0 - - - +
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Residues in contact with MET 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 TYR* 3.1 54.5 - - + +
250A THR 2.8 3.6 + - - +
252A MET* 1.3 86.1 - - + +
254A SER* 1.3 64.7 + - - +
256A LEU* 4.5 6.7 - - - +
257A PHE* 3.7 22.9 - - + -
309A ILE* 5.3 7.4 - - + -
310A PHE* 6.4 1.8 - - + -
313A ASN* 3.3 26.9 - - + +
428A VAL* 3.8 30.1 - - + -
429A TYR 5.1 0.2 - - - +
437A CYS* 5.4 7.2 - - + -
457A PHE* 5.4 1.0 - - - -
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Residues in contact with SER 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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250A THR 2.7 9.0 + - - -
251A ARG* 2.5 21.8 + - - +
253A MET* 1.3 72.4 - - - +
255A GLN* 1.3 67.6 + - - +
256A LEU 2.5 5.1 + - - -
257A PHE* 2.4 37.8 + - - +
258A LEU* 4.3 4.7 - - - -
457A PHE* 3.7 21.1 - - - -
622B GLN* 2.7 45.2 + - - -
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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 ARG* 3.0 36.2 + - + +
252A MET* 5.5 1.3 - - - -
254A SER* 1.3 83.2 + - - +
256A LEU* 1.3 57.8 + - + +
257A PHE 2.8 3.4 + - - +
258A LEU* 4.0 9.4 - - + +
259A ASP* 4.0 28.1 - - + +
260A THR* 2.7 33.4 + - - -
274B SER* 4.4 14.9 + - - +
622B GLN* 5.0 4.4 + - - +
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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