Contacts of the helix formed by residues 252 - 260 (chain B) in PDB entry 3ISL
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 ASP 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ARG* 2.8 33.4 + - - +
224B ARG 6.1 0.3 - - - -
246B ILE* 3.3 22.5 + - + +
248B SER 3.0 9.5 + - - +
249B ASN 3.3 17.0 + - - +
250B TYR 3.4 1.2 + - - -
251B PHE* 1.3 76.2 - - - +
253B LEU* 1.3 56.5 + - - +
254B SER* 2.6 32.7 + - - -
255B GLN* 3.3 17.4 + - - +
256B LEU* 2.8 30.4 + - - +
267B HIS* 4.5 0.7 + - - -
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Residues in contact with LEU 253 (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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67B TYR* 3.5 18.2 + - - +
69B ILE* 4.3 2.5 - - + -
79B ALA* 3.9 20.6 - - + +
80B VAL* 3.7 29.8 - - + -
83B SER* 3.4 25.7 - - - +
211B ILE* 3.8 13.0 - - + -
213B TYR* 4.1 12.1 - - + +
217B VAL* 5.8 0.2 - - + -
221B ILE* 3.8 25.6 - - + -
251B PHE 3.4 1.4 + - - +
252B ASP* 1.3 69.3 + - - +
254B SER* 1.3 52.3 + - - +
255B GLN 3.2 5.4 - - - -
256B LEU* 3.6 21.8 - - + -
257B GLU* 2.6 38.5 + - - +
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Residues in contact with SER 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ILE* 3.7 25.7 - - - +
222B ALA* 5.4 2.0 - - - -
224B ARG 3.9 20.7 + - - -
246B ILE* 5.5 0.9 - - - -
252B ASP* 2.6 25.1 + - - -
253B LEU* 1.3 77.2 - - - +
255B GLN* 1.3 59.8 + - - +
257B GLU* 3.8 13.4 - - - +
258B ASP* 3.5 21.8 - - - +
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Residues in contact with GLN 255 (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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105A GLU* 6.4 0.2 - - - -
109A ARG* 3.4 10.3 + - - +
249B ASN* 3.1 24.4 + - - +
252B ASP* 3.3 32.3 + - - +
254B SER* 1.3 78.9 + - - +
256B LEU* 1.3 62.8 + - - +
257B GLU 3.3 1.1 - - - -
258B ASP* 3.5 5.0 + - - +
259B TYR* 3.1 23.6 + - - +
265B LEU* 4.2 25.0 - - + +
267B HIS* 3.7 33.4 - - + +
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Residues in contact with LEU 256 (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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67B TYR* 3.9 13.5 - - + +
68B PRO 5.7 0.7 - - - +
69B ILE* 4.0 22.7 - - + -
79B ALA* 5.3 1.1 - - + -
250B TYR 3.6 19.5 - - - +
251B PHE* 4.4 3.6 - - - -
252B ASP 2.8 21.2 + - - +
253B LEU* 3.3 25.8 + - + -
255B GLN* 1.3 75.0 - - - +
257B GLU* 1.3 58.6 + - - +
259B TYR* 3.3 4.2 - - + +
260B TRP* 3.1 40.4 + - + +
267B HIS* 3.3 16.2 - - + +
268B HIS* 3.3 31.9 - - + +
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Residues in contact with GLU 257 (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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65B TRP* 3.9 25.5 + - + +
67B TYR* 3.9 6.7 + - - +
213B TYR* 2.8 38.0 + - - +
218B ALA* 4.5 9.9 - - - +
221B ILE* 4.1 13.7 - - - +
222B ALA* 5.2 6.8 - - - +
253B LEU 2.6 26.6 + - - +
254B SER* 3.8 17.9 - - - +
256B LEU* 1.3 72.2 - - - +
258B ASP* 1.3 60.7 + - - +
260B TRP* 3.3 14.5 + - - +
261B SER* 2.6 26.2 + - - -
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Residues in contact with ASP 258 (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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254B SER 3.5 16.6 - - - +
255B GLN* 3.5 7.4 + - - +
256B LEU 3.4 0.2 - - - -
257B GLU* 1.3 78.4 - - - +
259B TYR* 1.3 63.4 + - - +
261B SER* 3.4 13.3 + - - +
263B ARG* 4.0 27.5 + - - +
264B ARG 3.4 10.7 + - - -
265B LEU* 3.3 45.5 + - + +
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Residues in contact with TYR 259 (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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39B GLN* 3.0 36.0 + - + +
40B PHE* 5.1 5.4 - + - -
48B MET* 3.7 21.4 - - + +
255B GLN 3.1 14.7 + - - +
256B LEU* 3.3 13.7 - - + +
258B ASP* 1.3 76.3 - - - +
260B TRP* 1.3 79.0 + + + +
261B SER 3.3 1.3 + - - -
264B ARG* 2.9 29.8 + - + -
265B LEU 3.0 30.7 + - - +
266B ASN* 4.6 1.6 - - - -
267B HIS* 3.8 11.9 - - + -
268B HIS* 3.1 37.7 + - - +
270B GLU* 3.2 31.3 + - + +
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Residues in contact with TRP 260 (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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48B MET* 3.4 59.2 - - + -
51B THR* 5.2 1.3 - - - -
52B MET* 3.5 43.6 - - + +
65B TRP* 5.8 2.9 - - - -
67B TYR* 3.7 34.4 - + + -
68B PRO* 3.4 47.9 + - + -
256B LEU* 3.1 28.6 + - + +
257B GLU* 3.3 5.9 + - - +
259B TYR* 1.3 91.0 - + + +
261B SER* 1.3 60.8 + - - +
264B ARG* 3.6 7.0 - - - +
268B HIS* 4.7 2.8 + - - -
270B GLU* 3.6 23.3 + - - -
275B LEU* 4.1 13.0 - - + -
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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