Contacts of the helix formed by residues 252 - 260 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 5.5 1.0 - - - +
246A ILE* 3.2 22.5 + - + +
248A SER 3.2 11.7 + - - +
249A ASN 3.2 18.9 + - - +
250A TYR 3.3 2.0 + - - -
251A PHE* 1.3 73.7 - - - +
253A LEU* 1.3 56.3 + - - +
254A SER* 3.1 24.0 + - - -
255A GLN* 2.8 35.9 + - + +
256A LEU* 2.9 27.3 + - - +
267A HIS* 4.6 0.3 + - - -
109B ARG* 2.9 17.8 + - - +
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Residues in contact with LEU 253 (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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67A TYR* 3.6 9.7 + - - +
69A ILE* 4.1 9.2 - - + -
79A ALA* 3.8 26.2 - - + +
80A VAL* 3.8 25.1 - - + -
83A SER* 3.4 27.0 - - - +
211A ILE* 3.7 19.7 - - + -
213A TYR* 3.9 16.8 - - + +
217A VAL* 5.7 0.4 - - + -
221A ILE* 3.7 24.0 - - + -
251A PHE 3.1 7.6 + - - +
252A ASP* 1.3 71.6 + - - +
254A SER* 1.3 53.0 + - - +
256A LEU* 3.5 10.3 - - + -
257A GLU* 2.7 37.5 + - - +
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Residues in contact with SER 254 (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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221A ILE* 3.6 31.1 + - - +
222A ALA* 5.0 3.8 - - - -
224A ARG 4.0 14.0 + - - -
246A ILE* 4.6 1.3 - - - -
252A ASP* 3.1 16.9 + - - -
253A LEU* 1.3 79.6 - - - +
255A GLN* 1.3 59.5 + - - +
257A GLU* 3.6 15.9 + - - +
258A ASP* 4.0 14.2 + - - +
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Residues in contact with GLN 255 (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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249A ASN* 3.2 24.9 + - - +
252A ASP* 2.8 40.3 + - - +
254A SER* 1.3 76.8 - - - +
256A LEU* 1.3 61.2 + - - +
258A ASP 3.2 2.9 + - - -
259A TYR* 3.0 24.6 + - - +
265A LEU* 3.6 29.1 - - + +
267A HIS* 3.5 27.2 - - + +
109B ARG* 3.5 13.1 - - - +
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Residues in contact with LEU 256 (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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67A TYR* 4.0 15.7 - - + +
68A PRO 5.7 0.4 - - - +
69A ILE* 4.2 25.4 - - + -
250A TYR 3.3 25.6 - - - +
251A PHE* 4.4 2.2 - - + -
252A ASP 2.9 21.2 + - - +
253A LEU* 3.3 14.1 + - + +
255A GLN* 1.3 77.4 - - - +
257A GLU* 1.3 56.3 + - - +
259A TYR* 3.4 7.6 - - + +
260A TRP* 3.0 39.4 + - + +
267A HIS* 3.5 9.2 - - - +
268A HIS* 3.2 40.4 - - + +
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Residues in contact with GLU 257 (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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65A TRP* 3.6 26.8 + - + +
67A TYR* 4.0 6.0 + - + +
213A TYR* 2.6 39.4 + - - +
218A ALA* 4.5 10.8 - - - +
221A ILE* 4.5 10.2 - - - +
222A ALA* 5.5 4.5 + - - +
253A LEU 2.7 25.7 + - - +
254A SER* 3.6 20.6 + - - +
256A LEU* 1.3 74.4 - - - +
258A ASP* 1.3 57.1 + - - +
260A TRP* 3.4 10.7 + - - +
261A SER* 2.8 27.3 + - - -
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Residues in contact with ASP 258 (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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254A SER 4.2 10.3 - - - +
255A GLN 3.2 7.7 + - - +
257A GLU* 1.3 78.0 - - - +
259A TYR* 1.3 63.9 + - - +
261A SER* 3.6 12.0 + - - +
263A ARG* 4.0 17.9 + - + +
264A ARG 3.3 10.2 + - - -
265A LEU* 3.1 42.7 + - + +
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Residues in contact with TYR 259 (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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39A GLN* 2.6 38.1 + - + +
40A PHE* 4.9 4.9 - + - -
48A MET* 4.2 14.4 - - + +
255A GLN 3.0 12.3 + - - +
256A LEU* 3.4 18.6 - - + +
258A ASP* 1.3 78.0 - - - +
260A TRP* 1.3 71.3 + + - +
261A SER 3.3 1.0 + - - -
264A ARG* 3.3 26.0 + - + -
265A LEU* 2.7 31.9 - - - +
266A ASN* 4.5 0.9 - - - -
267A HIS* 3.6 11.4 - - + -
268A HIS* 2.8 46.6 + + - -
270A GLU* 3.1 26.5 + - + +
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Residues in contact with TRP 260 (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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48A MET* 3.2 48.7 - - + -
51A THR* 5.1 1.1 - - - -
52A MET* 2.8 63.0 - - + +
67A TYR* 3.4 34.4 - + + -
68A PRO* 3.3 47.4 + - + -
256A LEU* 3.0 26.6 + - + +
257A GLU 3.4 5.8 + - - +
259A TYR* 1.3 94.3 - + + +
261A SER* 1.3 60.4 + - - +
264A ARG* 3.7 2.5 - - - +
268A HIS* 4.6 3.0 + - - -
270A GLU* 3.5 25.4 + - + -
275A LEU* 3.9 15.0 - - + -
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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