Contacts of the helix formed by residues 247 - 252 (chain B) 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 CYS 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TRP* 3.5 22.7 - - + -
245B ILE* 2.9 10.7 + - - +
246B PHE* 1.3 77.1 - - - +
248B TYR* 1.3 64.5 + - - +
249B PRO* 3.1 9.6 - - - -
250B ARG* 2.8 21.7 + - + -
251B ILE* 3.1 7.8 + - + -
257B THR* 3.8 15.5 - - - -
258B VAL* 3.3 29.6 - - - -
803B SF4 2.3 34.3 - - - -
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Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TRP* 4.5 0.9 - - - -
32A GLU* 2.6 44.7 + - + +
35A TYR* 3.3 26.9 - + + +
36A ARG* 3.9 22.2 - - + -
204B ARG* 3.6 16.8 - - - +
209B ILE* 3.7 24.0 - - + -
211B LEU* 3.7 23.1 - - + -
245B ILE* 3.0 41.2 + - + -
246B PHE 3.0 4.9 + - - -
247B CYS* 1.3 75.1 - - - +
249B PRO* 1.3 71.4 - - + +
251B ILE* 3.8 3.6 - - - -
252B GLU* 2.9 46.6 + - - +
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Residues in contact with PRO 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 4.0 2.7 - - + +
36A ARG* 3.9 31.6 - - + +
39A TRP* 4.1 27.8 + - + -
30B TRP* 3.9 20.2 - - + -
245B ILE* 4.5 0.9 - - + -
247B CYS* 3.1 9.2 - - - -
248B TYR* 1.3 109.4 - - + +
250B ARG* 1.3 59.3 + - + +
252B GLU* 4.0 17.3 - - - +
253B ALA* 4.4 6.2 + - - +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TRP* 3.3 52.9 - - + +
60A LYS* 4.8 7.1 - - - +
62A TYR* 4.8 6.0 + - - -
72A THR* 6.2 1.6 - - - +
30B TRP* 5.8 1.1 - - + -
247B CYS* 2.8 14.2 + - + +
249B PRO* 1.3 77.9 - - + +
251B ILE* 1.3 65.1 + - + +
252B GLU 3.1 2.0 - - - -
253B ALA* 3.0 12.9 + - - +
255B GLN* 3.0 48.6 + - + +
256B PRO* 3.0 31.8 + - - +
257B THR 3.8 11.1 + - - -
258B VAL* 4.1 20.4 - - - +
261B GLU* 2.8 33.5 + - - +
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Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.5 15.5 - - + -
207B ASP* 4.5 4.0 - - + +
209B ILE* 4.3 15.3 - - + -
246B PHE* 3.3 38.1 - - + +
247B CYS* 3.1 9.3 + - + +
248B TYR* 4.1 7.4 - - - +
250B ARG* 1.3 74.3 - - - +
252B GLU* 1.3 59.6 + - + +
254B GLY* 2.8 17.5 + - - -
255B GLN 3.4 21.3 - - - +
256B PRO 3.9 0.4 - - - -
257B THR* 3.5 26.5 - - + +
270B LEU* 5.8 0.7 - - + -
458B VAL* 4.1 15.9 - - + +
459B PRO 3.5 12.8 - - - +
461B SER* 4.1 12.1 + - - +
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 5.1 0.3 + - - -
36A ARG* 2.7 49.2 + - - -
204B ARG* 2.8 33.1 + - - +
207B ASP* 4.7 0.2 - - - +
248B TYR* 2.9 26.1 + - + +
249B PRO* 4.0 8.9 - - - +
251B ILE* 1.3 77.3 - - - +
253B ALA* 1.3 56.8 + - + +
460B SER* 3.4 6.6 + - - -
461B SER* 2.9 38.1 + - - +
462B HIS 4.1 1.2 + - - -
463B ARG* 3.5 26.4 + - + +
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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