Contacts of the strand formed by residues 52 - 56 (chain B) in PDB entry 5ICN
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 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A GLN* 2.8 11.1 - - - +
199A TRP 3.5 7.0 - - - -
200A GLU* 2.7 43.3 - - - +
201A ALA* 3.4 13.5 + - + -
202A HIS* 3.2 19.9 + - + -
10B LYS* 3.9 19.2 + - + +
11B VAL 3.0 16.8 + - - +
12B CYS* 3.3 8.3 - - - -
13B TYR 2.8 30.9 + - - +
51B MET* 1.3 70.7 - - - +
53B ILE* 1.3 55.4 + - - +
54B TYR* 3.6 23.3 - - + -
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLN* 3.7 3.1 - - - +
198A VAL* 2.7 40.2 + - + +
199A TRP* 3.0 32.1 + - + +
13B TYR* 3.4 33.7 - - + +
15B TYR* 5.4 3.4 - - + +
39B HIS* 4.9 4.3 - - + -
48B TYR* 3.6 49.4 - - + +
51B MET* 3.4 28.5 - - + +
52B GLU* 1.3 69.6 - - - +
54B TYR* 1.3 64.0 + - - +
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Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU* 3.6 26.9 - - + -
196A THR 4.0 1.1 - - - -
197A GLN* 3.5 49.0 + - + -
198A VAL* 5.0 1.1 - - - -
12B CYS* 4.2 6.3 - - + -
13B TYR 2.8 10.0 + - - +
14B TYR* 3.3 38.4 - + + -
15B TYR 3.0 26.5 + - - +
52B GLU* 3.6 34.5 + - + +
53B ILE* 1.3 76.0 - - - +
55B ARG* 1.3 58.8 + - - +
56B PRO* 3.5 1.2 - - - +
123B LYS* 3.0 33.5 + - - -
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Residues in contact with ARG 55 (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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195A GLU* 3.3 4.0 - - - -
196A THR* 3.0 66.3 + - - +
198A VAL* 4.3 14.2 - - + +
15B TYR 3.6 9.2 - - - +
16B ASP* 3.4 28.5 + - - +
54B TYR* 1.3 71.4 - - - +
56B PRO* 1.3 73.8 + - + +
57B HIS* 3.3 32.4 + - - +
58B LYS* 6.2 1.0 - - - +
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Residues in contact with PRO 56 (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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194A LEU 3.6 6.5 - - - +
195A GLU* 4.5 0.7 - - - -
14B TYR* 4.3 9.4 - - + -
15B TYR* 3.4 28.3 - - - +
16B ASP* 4.1 7.9 - - + +
54B TYR 3.5 7.0 - - - +
55B ARG* 1.3 94.4 + - + +
57B HIS* 1.3 65.3 + - - +
58B LYS 3.8 0.5 + - - -
112B LEU* 4.2 23.3 - - + +
115B GLY* 3.9 7.4 - - - +
116B GLY* 3.7 33.7 - - - +
134B ASN* 5.9 0.7 - - - +
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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