Contacts of the helix formed by residues 248 - 253 (chain A) in PDB entry 4I6H
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A TYR 3.5 2.8 + - - -
247A LEU* 1.3 75.1 - - - +
249A PRO* 1.4 73.8 - - - +
250A GLU* 3.5 13.9 - - - +
251A VAL* 3.2 32.0 + - - +
252A LEU* 3.2 23.6 + - - +
257A HIS* 5.8 0.6 - - - -
261A SER* 3.4 20.3 + - - -
264A TRP* 3.7 16.8 - - - -
292A ILE* 4.2 1.3 - - - -
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Residues in contact with PRO 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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248A SER* 1.4 84.0 - - - +
250A GLU* 1.3 70.8 + - - +
252A LEU* 3.3 13.0 + - + +
253A ASN* 3.2 29.2 + - - +
264A TRP* 3.5 35.4 - - + -
292A ILE* 3.2 21.7 - - - +
293A ARG* 3.3 26.3 - - + +
295A ALA* 4.5 2.5 - - + -
317A LYS 3.9 13.0 - - - +
322A ARG* 3.7 6.1 - - - +
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Residues in contact with GLU 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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248A SER* 3.5 4.0 - - - +
249A PRO* 1.3 75.5 - - - +
251A VAL* 1.3 66.4 + - - +
253A ASN* 3.2 16.2 + - - +
255A GLN* 3.2 33.1 + - + +
256A GLY 4.0 8.3 - - - +
258A GLY* 5.4 1.1 - - - +
260A GLU* 4.1 0.9 - - - +
261A SER* 3.0 31.4 + - - +
317A LYS 5.4 0.2 + - - -
319A PRO* 3.6 32.0 - - + +
322A ARG* 2.6 49.1 + - - -
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Residues in contact with VAL 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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238A ARG 4.4 5.0 - - - +
239A THR 5.7 0.4 - - - +
240A ILE* 3.7 31.5 - - + +
241A CYS 5.5 0.4 - - - +
247A LEU* 4.1 18.6 - - + -
248A SER* 3.2 26.1 + - - +
250A GLU* 1.3 75.2 - - - +
252A LEU* 1.3 62.0 + - + +
254A LYS* 3.2 22.9 + - - -
256A GLY* 3.4 30.3 - - - +
257A HIS* 3.8 25.6 - - + -
261A SER* 4.3 0.2 - - - +
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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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240A ILE* 4.5 7.0 - - + -
247A LEU* 3.8 32.5 - - + +
248A SER 3.2 16.8 - - - +
249A PRO 3.5 6.3 - - - +
250A GLU 3.2 0.4 - - - -
251A VAL* 1.3 76.2 - - - +
253A ASN* 1.3 55.4 + - - +
254A LYS* 3.3 13.1 + - - +
289A TYR* 3.8 40.8 - - + +
292A ILE* 3.7 30.7 - - + -
293A ARG* 2.8 47.5 + - + +
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Residues in contact with ASN 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 PRO* 3.2 22.1 + - - +
250A GLU* 3.2 11.9 + - - +
251A VAL 3.2 1.2 - - - -
252A LEU* 1.3 76.8 - - - +
254A LYS* 1.3 71.0 + - - +
255A GLN* 3.2 24.3 + - + +
293A ARG* 3.4 30.3 + - - +
317A LYS* 6.2 1.2 - - - +
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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