Contacts of the strand formed by residues 37 - 42 (chain F) in PDB entry 3E2A
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 TYR 37 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D LYS* 3.7 36.1 + - + +
4D ILE* 4.2 13.7 - - + -
7D LEU* 4.4 9.9 - - + +
35F PRO 3.7 0.6 - - - -
36F HIS* 1.3 94.5 + + + +
38F LEU* 1.3 59.5 + - - +
55F LEU* 4.0 24.2 - - + +
59F GLU* 3.3 22.4 + - - -
60F LEU* 3.5 25.2 - - + -
61F PHE* 2.9 28.1 + - - +
90F ILE* 3.7 6.7 - - - +
92F HIS* 3.4 37.5 - + + +
94F ILE* 4.1 21.1 - - + -
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Residues in contact with LEU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F TYR* 1.3 74.1 - - - +
39F TRP* 1.3 67.6 + - - +
40F ILE* 4.1 8.3 - - + -
61F PHE* 3.2 25.8 - - + +
63F HIS 4.3 3.1 - - - +
80F VAL* 3.5 24.0 - - + -
81F VAL* 3.9 27.8 - - + -
84F ALA* 3.6 30.7 - - + -
90F ILE* 3.5 3.0 - - + +
92F HIS 3.0 12.3 + - - +
93F ILE* 3.4 26.6 - - + -
94F ILE* 2.8 30.3 + - - +
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Residues in contact with TRP 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 4.9 0.7 - - + -
37F TYR 4.0 0.6 - - - -
38F LEU* 1.3 72.4 - - - +
40F ILE* 1.3 62.1 + - - +
41F GLY* 3.7 19.2 - - - -
49F ALA* 3.4 31.6 - - + +
52F LEU* 4.4 9.0 - - + -
53F THR* 4.0 29.8 - - + -
60F LEU* 4.1 16.6 - - + -
61F PHE 2.8 13.0 + - - +
62F VAL* 3.4 20.6 - - + -
63F HIS 2.9 28.8 + - - +
64F ARG* 5.4 2.1 - - + +
94F ILE* 3.4 40.8 - - + -
96F CYS* 3.3 41.3 - - + +
179F TRP* 4.0 11.2 - + - -
188F LEU* 4.6 4.9 - - + -
232F BCT 5.3 2.1 + - - -
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Residues in contact with ILE 40 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F LEU* 4.1 14.6 - - + -
39F TRP* 1.3 76.7 - - - +
41F GLY* 1.3 60.6 + - - +
63F HIS* 3.2 26.5 - - + -
65F ASN* 4.5 0.7 - - - +
68F ASN* 4.0 14.9 - - - +
69F GLN 4.4 13.0 - - - +
70F VAL* 4.0 16.8 - - + -
77F CYS* 4.0 19.7 - - - -
80F VAL* 6.0 0.2 - - + -
81F VAL* 4.2 13.7 - - + -
93F ILE* 4.1 18.2 - - + -
94F ILE 2.7 13.5 + - - +
95F ILE* 3.3 13.1 - - + +
96F CYS 2.8 26.7 + - - +
158F LEU* 4.8 1.6 - - + -
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Residues in contact with GLY 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F TRP* 3.7 17.7 - - - -
40F ILE* 1.3 75.3 - - - +
42F CYS* 1.3 60.9 + - - -
45F SER* 5.3 0.9 - - - -
63F HIS 2.9 8.9 + - - +
64F ARG* 3.2 9.9 - - - -
65F ASN 3.1 22.3 + - - +
68F ASN* 3.5 12.7 - - - -
96F CYS 3.5 11.2 - - - -
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Residues in contact with CYS 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F GLY* 1.3 73.4 - - - -
43F SER* 1.3 61.7 + - - +
44F ASP* 3.2 14.6 - - - -
45F SER* 3.1 18.1 + - - -
64F ARG* 2.8 24.2 - - - -
65F ASN 3.1 5.2 - - - +
66F VAL* 4.3 1.8 - - - -
67F ALA 3.3 21.1 - - - -
68F ASN* 3.5 19.3 - - - +
96F CYS 3.9 2.2 + - - -
98F HIS* 3.6 10.8 - - + +
101F CYS* 3.8 0.2 - - - -
230F ZN 2.3 37.2 - - - -
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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