Contacts of the helix formed by residues 239 - 244 (chain A) in PDB entry 1SIW
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 GLU 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A HIS* 4.3 4.0 + - - -
237A VAL 3.8 0.8 + - - -
238A PRO* 1.3 76.9 - - - +
240A SER* 1.3 68.0 + - - +
241A ALA* 3.8 17.8 - - - +
242A ASP* 2.9 24.9 + - - +
243A TRP* 3.8 5.7 + - - -
577A TYR* 4.3 0.9 - - - -
584A ARG* 5.7 1.6 - - - +
801A ASP 3.7 9.4 - - - +
802A MET 3.3 14.7 - - - +
803A HIS* 4.0 4.5 - - - -
804A PRO* 3.3 29.5 - - - +
1005A LYS* 5.7 3.6 + - - -
1016A GLU* 5.4 0.5 - - - +
1021A SER* 3.7 9.2 + - - -
1022A TYR* 3.1 47.9 + - + +
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Residues in contact with SER 240 (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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87A HIS* 4.4 2.1 - - - -
238A PRO 4.0 0.2 + - - -
239A GLU* 1.3 71.5 - - - +
241A ALA* 1.3 64.5 + - - +
243A TRP* 3.0 38.9 + - - +
263A ASP* 2.6 45.3 + - - -
266A PHE* 3.4 23.5 - - - +
802A MET* 3.0 25.9 + - - +
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Residues in contact with ALA 241 (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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80A THR* 4.9 7.2 - - + -
84A LEU* 4.0 10.2 - - + +
85A PRO 5.6 0.2 - - - +
87A HIS* 4.3 10.3 - - + +
239A GLU* 3.1 24.2 - - - +
240A SER* 1.3 81.2 + - - +
242A ASP* 1.3 56.7 + - - +
244A TYR* 3.0 27.5 + - - +
245A ASN* 4.0 5.8 + - - -
266A PHE* 3.8 26.7 - - + -
802A MET 4.4 0.4 + - - -
1021A SER* 4.6 6.1 - - - +
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Residues in contact with ASP 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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238A PRO* 3.6 7.6 - - + +
239A GLU* 2.9 16.5 + - + +
241A ALA* 1.3 76.0 - - - +
243A TRP* 1.3 64.9 + - - +
244A TYR 2.9 2.2 - - - -
245A ASN* 2.9 31.3 + - - +
537A MET* 3.9 2.9 - - - +
570A SER* 2.8 24.8 + - - -
571A GLY* 3.0 17.2 + - - -
1021A SER* 3.2 11.7 - - - -
1022A TYR 3.6 20.6 - - - +
1023A ASN* 2.8 30.1 + - - -
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Residues in contact with TRP 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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238A PRO* 5.1 0.4 - - + -
239A GLU 3.8 5.8 - - - -
240A SER* 3.0 17.5 + - - +
242A ASP* 1.3 77.7 - - - +
244A TYR* 1.3 57.7 + - - +
245A ASN 3.1 0.2 - - - -
246A SER* 3.0 23.0 + - - -
249A ILE* 3.9 14.8 - - + +
256A VAL* 3.9 27.1 - - + -
260A ARG* 4.4 3.1 - - + -
263A ASP* 3.3 38.4 - - + -
266A PHE* 3.8 21.5 - - + +
267A PHE* 3.9 17.3 - - + -
270A VAL* 3.8 9.4 - - - +
537A MET* 3.6 29.1 - - + -
539A ILE* 3.9 19.1 - - + +
577A TYR* 3.0 44.1 + + - -
802A MET* 3.8 14.8 - - + -
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Residues in contact with TYR 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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83A ASP 3.6 13.5 - - - -
84A LEU* 3.7 22.4 - - + -
85A PRO* 3.6 32.5 - - + -
240A SER 4.1 0.2 + - - -
241A ALA 3.0 16.2 + - - +
242A ASP 2.9 0.2 - - - -
243A TRP* 1.3 80.3 - - - +
245A ASN* 1.3 57.1 + - - +
246A SER 3.3 1.6 + - - +
266A PHE* 3.9 15.4 + + + +
269A GLU* 3.7 7.2 + - + -
270A VAL* 3.5 44.2 - - + +
273A LYS* 2.9 39.6 + - + +
444B TYR* 2.7 37.7 + - - -
448B ALA* 3.4 15.9 - - - +
449B ILE* 3.8 3.7 - - + +
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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