Contacts of the helix formed by residues 246 - 253 (chain A) in PDB entry 5J1T
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A SER 3.3 17.1 + - - +
242A VAL* 3.1 22.5 + - - +
243A SER* 3.0 19.7 + - - +
244A VAL 3.5 0.4 - - - -
245A PHE* 1.3 78.6 - - - +
247A ASN* 1.3 60.8 + - - +
248A LYS* 3.6 8.0 + - - +
249A ASN* 3.1 23.7 + - - +
250A SER* 2.9 30.4 + - - -
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Residues in contact with ASN 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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245A PHE 5.2 1.2 - - - +
246A ASN* 1.3 77.9 - - - +
248A LYS* 1.3 53.9 + - - +
250A SER* 3.6 8.5 + - - -
251A GLY* 2.7 32.6 + - - -
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Residues in contact with LYS 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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246A ASN* 3.3 10.6 + - - +
247A ASN* 1.3 77.8 - - - +
249A ASN* 1.3 63.0 + - - +
251A GLY* 3.3 3.0 + - - -
252A PHE* 2.9 26.0 + - + +
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Residues in contact with ASN 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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243A SER 2.5 31.3 + - - -
244A VAL* 3.5 22.2 + - - +
246A ASN* 3.1 13.7 + - - +
248A LYS* 1.3 78.8 - - - +
250A SER* 1.3 65.7 + - - +
251A GLY 3.2 0.2 - - - -
252A PHE* 3.2 8.5 + - - +
253A TRP* 3.0 37.0 + - + +
261A ASN* 5.2 0.2 + - - -
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Residues in contact with SER 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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244A VAL 5.1 0.4 + - - -
245A PHE* 4.0 11.4 + - - -
246A ASN 2.9 21.2 + - - -
247A ASN* 3.6 11.0 + - - -
249A ASN* 1.3 72.9 - - - +
251A GLY* 1.3 65.4 + - - +
253A TRP 3.5 1.4 + - - -
254A HIS* 3.1 28.3 + - - +
261A ASN* 4.7 15.8 + - - +
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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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247A ASN 2.7 21.6 + - - -
248A LYS* 3.6 3.6 - - - -
250A SER* 1.3 74.5 - - - +
252A PHE* 1.3 62.3 + - - +
254A HIS* 3.1 21.3 + - - +
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Residues in contact with PHE 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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172A MET* 5.1 1.3 - - + -
177A ALA* 4.0 25.6 - - + -
180A ILE* 3.8 23.1 - - + -
181A ASP* 3.4 15.3 - - - -
184A LYS* 2.8 58.6 + - - +
248A LYS* 2.9 16.3 + - + +
249A ASN* 3.2 13.4 + - - +
251A GLY* 1.3 76.5 - - - +
253A TRP* 1.3 91.6 + + - +
254A HIS 3.5 2.3 + - - +
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Residues in contact with TRP 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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172A MET* 3.1 33.3 - - + +
180A ILE* 3.4 24.0 - - + -
184A LYS* 4.8 4.0 - - - -
187A LEU* 3.9 15.3 - - + -
205A PHE* 3.7 32.5 - + - -
244A VAL 6.0 0.4 - - - -
249A ASN* 3.0 32.9 + - + +
250A SER 3.7 1.8 - - - -
252A PHE* 1.3 97.1 - + + +
254A HIS* 1.3 60.9 + - - +
261A ASN* 3.3 22.6 - - - +
262A LEU* 2.8 47.5 + - + +
263A ILE* 3.5 28.7 - - + +
266A PHE* 5.3 5.8 - + - -
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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