Contacts of the helix formed by residues 241 - 251 (chain A) in PDB entry 1W4X
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 ARG 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A ASP 4.0 10.3 - - - +
238A LEU* 3.0 17.9 + - + +
240A LYS* 1.3 78.8 - - + +
242A TYR* 1.3 66.4 + - - +
243A ALA* 3.3 2.7 - - - -
244A GLU* 3.1 44.7 + - - +
245A PHE* 3.0 41.3 + - - +
248A GLU* 3.0 35.4 + - - -
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Residues in contact with TYR 242 (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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70A ILE* 2.9 40.4 + - - +
73A CYS* 3.4 12.5 - - - -
78A GLU* 5.0 1.3 - - - +
81A LEU* 3.6 55.0 - - + -
82A GLN* 4.9 2.5 - - - +
86A TRP* 4.4 9.7 + + - -
235A LEU* 4.8 6.7 - - + -
238A LEU* 2.9 28.3 + - + +
239A LYS* 3.7 34.0 + - + +
241A ARG* 1.3 76.5 - - - +
243A ALA* 1.3 56.5 + - - +
245A PHE* 3.3 20.3 + + - +
246A ARG* 2.9 34.6 + - + +
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Residues in contact with ALA 243 (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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78A GLU* 4.3 17.7 + - - +
81A LEU* 5.2 3.8 - - + +
241A ARG 3.3 1.2 - - - -
242A TYR* 1.3 77.9 - - - +
244A GLU* 1.3 60.9 + - - +
246A ARG* 3.5 3.3 + - - +
247A GLU* 3.1 24.8 + - - +
250A ARG* 4.9 2.3 + - - -
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Residues in contact with GLU 244 (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 ARG* 3.1 49.8 + - + +
243A ALA* 1.3 77.4 - - - +
245A PHE* 1.3 61.2 + - - +
247A GLU* 3.4 6.5 + - - +
248A GLU* 3.1 33.7 + - + +
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Residues in contact with PHE 245 (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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70A ILE* 3.6 39.5 - - + -
71A GLU* 3.6 22.0 - - - -
234A PHE* 6.0 1.6 - + - -
238A LEU* 3.6 28.9 - - + -
241A ARG* 3.0 30.5 + - - +
242A TYR* 3.5 17.7 - + - +
244A GLU* 1.3 77.3 - - - +
246A ARG* 1.3 67.1 + - + +
248A GLU* 3.2 8.9 + - - +
249A SER 3.2 6.2 + - - -
257A HIS* 3.1 62.5 - + + -
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Residues in contact with ARG 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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70A ILE 4.3 7.6 - - - -
71A GLU* 3.6 17.5 + - - +
73A CYS* 2.8 45.1 + - - -
75A SER* 3.6 30.0 + - - -
81A LEU* 6.2 0.4 - - + -
242A TYR* 2.9 25.1 + - + +
243A ALA* 4.4 3.1 - - - +
245A PHE* 1.3 77.8 - - + +
247A GLU* 1.3 60.3 + - - +
249A SER* 3.3 7.4 + - - -
250A ARG* 3.1 42.1 + - - +
447A LEU* 4.0 18.2 - - - +
448A VAL* 3.6 22.3 - - - +
451A GLU* 3.1 23.0 + - - -
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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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243A ALA 3.1 17.8 + - - +
244A GLU* 3.8 7.2 - - - +
246A ARG* 1.3 73.8 - - - +
248A GLU* 1.3 64.3 + - - +
250A ARG* 2.7 40.1 + - - +
251A ASN* 2.5 54.8 + - - +
525A ARG* 3.4 15.1 + - - -
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Residues in contact with GLU 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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241A ARG* 3.0 32.7 + - - -
244A GLU* 3.1 23.4 + - + +
245A PHE* 3.2 9.5 + - - +
247A GLU* 1.3 76.6 - - - +
249A SER* 1.3 60.5 + - - +
251A ASN* 3.1 16.5 + - - +
252A THR* 3.2 15.7 - - - +
257A HIS* 2.7 38.4 + - + +
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Residues in contact with SER 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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71A GLU* 2.7 28.4 + - - -
245A PHE* 3.2 8.2 + - - -
246A ARG* 3.3 17.8 + - - -
248A GLU* 1.3 75.6 - - - +
250A ARG* 1.3 59.4 + - - +
252A THR* 2.8 28.3 + - - -
255A GLY* 3.2 24.0 - - - -
256A THR* 4.2 0.6 - - - +
257A HIS* 3.0 21.5 + - - -
448A VAL* 4.6 5.4 - - - -
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Residues in contact with ARG 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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75A SER* 3.1 32.1 + - - -
243A ALA 4.9 2.4 + - - -
246A ARG* 3.1 25.4 + - - +
247A GLU* 2.7 56.4 + - - +
248A GLU 3.3 0.4 - - - -
249A SER* 1.3 76.1 - - - +
251A ASN* 1.3 56.7 + - - +
252A THR 3.3 2.5 + - - -
448A VAL* 4.5 14.4 - - + -
451A GLU* 4.7 4.2 + - - +
455A GLU* 5.6 5.9 + - - -
521A PHE* 3.4 32.9 - - + -
522A HIS* 3.9 5.7 + - - +
525A ARG* 3.5 35.5 + - - +
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Residues in contact with ASN 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 GLU* 2.5 46.4 + - - +
248A GLU* 3.1 10.4 + - - +
249A SER 3.1 1.4 - - - -
250A ARG* 1.3 76.8 - - - +
252A THR* 1.3 63.7 + - - +
522A HIS* 3.0 42.2 + - + +
525A ARG* 3.4 6.0 + - - +
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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