Contacts of the strand formed by residues 65 - 69 (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 TRP 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B MET* 4.8 1.6 - - + -
63B ASN* 3.1 1.9 - - - +
64B ARG* 1.3 130.2 - - + +
66B ALA* 1.3 53.6 + - - +
67B TYR* 4.2 12.3 - + + -
211B ILE 4.4 0.2 - - - -
212B THR* 2.7 26.7 + - - -
213B TYR* 3.0 66.5 + + + +
214B ASN* 3.9 5.6 - - - -
215B GLU* 3.7 47.1 - - + -
218B ALA* 3.9 16.6 - - + -
257B GLU* 3.9 25.0 + - + +
260B TRP 5.8 3.6 - - - -
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B MET* 3.1 44.3 - - - +
55B LEU* 3.9 17.0 - - + -
56B ARG* 3.9 21.5 - - + +
63B ASN 4.7 0.2 - - - +
64B ARG 3.6 4.6 + - - -
65B TRP* 1.3 74.3 - - - +
67B TYR* 1.3 65.7 + - - +
211B ILE 3.2 7.2 - - - +
212B THR* 3.8 12.8 - - - +
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Residues in contact with TYR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B MET* 4.1 11.4 - - + -
55B LEU* 3.8 7.2 - - - +
65B TRP* 4.2 11.9 - + + -
66B ALA* 1.3 83.4 - - - +
68B PRO* 1.4 79.4 - - + +
69B ILE* 3.9 10.3 - - + -
211B ILE* 2.8 58.7 + - + +
213B TYR* 2.9 36.1 + + - -
253B LEU* 3.5 26.7 + - - +
256B LEU* 4.1 17.9 - - + -
257B GLU* 3.9 7.3 + - - -
260B TRP* 3.7 37.9 - + + -
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Residues in contact with PRO 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 4.8 2.7 - - + -
52B MET* 5.4 0.7 - - + -
55B LEU* 4.0 10.3 - - + -
67B TYR* 1.4 91.4 - - + +
69B ILE* 1.3 65.1 + - - +
70B ASP* 4.5 0.6 - - - +
208B MET* 4.0 17.3 - - + -
209B ALA 3.6 7.9 - - - +
210B PRO* 3.9 4.0 - - + -
256B LEU* 5.7 0.5 - - - +
260B TRP* 3.4 53.2 + - + -
268B HIS* 5.9 0.2 - - - -
270B GLU* 4.0 7.6 - - - +
275B LEU* 4.1 6.5 - - + -
278B LEU* 3.8 27.6 - - + -
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Residues in contact with ILE 69 (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 11.2 - - + -
68B PRO* 1.3 79.4 - - - +
70B ASP* 1.3 68.4 + - - +
71B GLY 2.9 18.4 + - - +
75B ALA* 3.9 12.1 - - + +
76B GLY* 3.7 22.0 - - - +
79B ALA* 4.6 2.9 - - + -
208B MET* 3.5 4.2 - - - +
209B ALA* 2.8 36.7 + - + +
211B ILE* 3.9 27.1 - - + -
250B TYR* 4.8 2.7 - - + -
251B PHE* 3.8 31.9 - - + -
253B LEU* 4.3 2.9 - - + -
256B LEU* 4.0 24.2 - - + -
268B HIS* 6.2 0.9 - - - -
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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