Contacts of the strand formed by residues 47 - 53 (chain B) in PDB entry 3IEU
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 ILE 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 4.6 0.2 - - + -
43B THR* 4.4 5.5 - - - +
45B HIS* 2.9 34.5 + - + +
46B ARG* 1.3 77.7 - - - +
48B VAL* 1.3 63.4 + - - +
49B GLY 3.7 17.3 - - - +
50B ILE* 4.1 13.7 - - + -
59B ILE* 3.9 15.5 - - + -
60B TYR 3.6 7.2 - - - +
61B VAL* 4.1 12.8 - - + -
74B ILE* 4.1 19.1 - - + -
77B LEU* 3.9 12.8 - - + -
180B PHE* 3.7 30.3 - - + -
186B THR* 4.3 18.0 + - - +
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Residues in contact with VAL 48 (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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13B ILE* 5.5 5.2 - - + -
25B LEU* 3.2 34.3 - - + +
29B LEU* 5.0 1.0 - - - +
43B THR* 6.1 2.5 - - + -
46B ARG 4.1 3.4 - - - +
47B ILE* 1.3 77.0 - - - +
49B GLY* 1.3 58.7 + - - +
60B TYR* 2.8 31.0 + - + +
61B VAL 4.1 6.5 - - - +
62B ASP* 3.8 31.0 - - + +
186B THR* 4.8 5.2 + - - -
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Residues in contact with GLY 49 (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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25B LEU* 4.3 8.1 - - - -
29B LEU* 4.2 13.2 - - - -
47B ILE* 3.6 5.1 - - - +
48B VAL* 1.3 82.2 - - - +
50B ILE* 1.3 63.2 + - - +
60B TYR* 2.8 37.3 + - - +
186B THR* 4.8 5.6 + - - -
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Residues in contact with ILE 50 (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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29B LEU* 3.7 12.6 - - - +
47B ILE* 4.1 7.6 - - + -
49B GLY* 1.3 79.6 - - - +
51B HIS* 1.3 60.1 + - - +
52B THR* 3.8 20.1 + - - +
57B GLN* 3.9 18.6 - - + +
58B ALA 3.4 9.6 - - - +
59B ILE* 4.3 8.3 - - + -
180B PHE* 3.7 38.6 - - + -
181B PRO 5.7 1.1 - - - +
182B GLU 5.6 3.5 - - - +
184B TYR* 4.8 7.0 - - + +
186B THR* 3.5 30.5 - - + +
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Residues in contact with HIS 51 (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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28B LEU 3.6 16.7 + - - +
29B LEU* 3.5 32.6 + - + +
30B GLY* 5.6 1.0 - - - -
49B GLY 4.3 0.2 - - - -
50B ILE* 1.3 71.5 - - - +
52B THR* 1.3 64.3 + - - +
53B GLU* 3.8 42.2 + - + +
56B TYR* 3.4 3.6 + - - +
57B GLN* 3.2 1.9 - - - -
58B ALA* 2.7 43.4 + - + +
60B TYR* 4.0 23.6 + - + -
170B ARG* 4.4 12.6 + - - -
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Residues in contact with THR 52 (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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81A ALA* 3.8 20.2 - - + -
50B ILE* 3.8 10.6 + - - +
51B HIS* 1.3 78.8 - - - +
53B GLU* 1.3 63.0 - - - +
56B TYR 3.2 3.4 - - - -
57B GLN* 3.0 26.9 + - - +
178B HIS* 4.0 13.5 - - + +
182B GLU* 3.6 46.3 + - + +
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Residues in contact with GLU 53 (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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51B HIS* 3.8 25.8 + - + +
52B THR* 1.3 75.4 - - - +
54B GLY* 1.3 65.8 + - - +
55B ALA 3.1 1.0 + - - -
56B TYR* 2.8 31.1 + - - +
170B ARG* 2.5 33.2 + - - +
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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