Contacts of the helix formed by residues 245 - 250 (chain A) in PDB entry 3NPC
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 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A PRO* 1.3 79.4 - - - +
246A ALA* 1.3 58.5 - - - +
247A GLU* 3.6 14.0 + - - +
248A PHE* 3.2 23.2 + - - +
249A MET* 3.0 26.7 + - - +
305A ASP* 4.6 6.2 + - - +
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A SER* 1.3 72.4 - - - +
247A GLU* 1.3 54.1 + - - +
249A MET* 3.2 12.5 + - - +
250A ALA* 2.8 35.9 + - - +
257A ARG* 4.9 3.5 + - - +
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Residues in contact with GLU 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 SER* 3.6 12.0 + - - +
246A ALA* 1.3 78.2 - - - +
248A PHE* 1.3 59.8 + - - +
250A ALA* 3.5 16.1 + - - +
251A ALA* 3.9 5.9 + - - +
305A ASP* 3.8 16.0 - - - +
307A ASP* 5.6 2.9 - - - +
308A LYS* 3.9 22.3 + - - -
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Residues in contact with PHE 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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194A PRO* 4.7 5.2 - - + -
195A GLU 5.3 1.1 - - - -
198A LEU* 3.9 25.4 - - + -
200A MET* 3.8 30.6 - - + +
234A TRP* 4.1 0.4 - + - -
244A PRO* 3.5 34.1 - - + -
245A SER* 3.2 18.7 + - - +
247A GLU* 1.3 76.5 - - - +
249A MET* 1.3 70.6 + - + +
251A ALA* 3.1 21.5 + - + +
252A LEU* 4.0 11.1 + - + +
304A ILE* 3.6 29.8 - - + -
305A ASP* 3.8 36.7 + - + +
306A PRO* 4.2 5.4 - - + -
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Residues in contact with MET 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 THR* 3.4 32.8 - - + -
244A PRO* 3.7 14.1 - - + +
245A SER 3.0 19.3 + - - +
246A ALA* 3.7 9.9 - - - +
248A PHE* 1.3 83.8 - - + +
250A ALA* 1.3 56.7 + - - +
252A LEU* 3.1 34.0 + - + +
257A ARG* 3.4 16.0 - - + +
260A VAL* 3.5 39.0 - - + +
261A GLU* 3.9 31.0 - - + +
265A LYS* 4.7 7.2 - - - +
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Residues in contact with ALA 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 ALA 2.8 17.7 + - - +
247A GLU* 3.5 11.0 - - - +
248A PHE 3.1 0.4 - - - -
249A MET* 1.3 76.8 - - - +
251A ALA* 1.3 56.5 + - - +
252A LEU 3.3 6.2 + - - +
257A ARG* 3.8 28.1 + - - +
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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