Contacts of the strand formed by residues 45 - 52 (chain B) in PDB entry 3EOA
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 LEU 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 5.5 1.1 - - + -
38A GLN* 5.6 0.2 - - - +
44A PRO* 3.7 19.1 - - + -
87A TYR* 3.5 49.5 - - + -
98A PHE* 3.3 58.2 + - + +
37B VAL* 3.9 6.1 - - + -
38B ARG 3.5 4.9 - - - -
39B GLN* 3.9 13.9 - - + +
44B GLY* 1.3 74.4 - - - -
46B GLU* 1.3 61.9 + - - +
95B TYR* 5.9 2.2 - - + -
111B TRP* 3.6 26.2 - - + -
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Residues in contact with GLU 46 (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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98A PHE* 4.5 0.2 - - - -
37B VAL* 3.4 4.3 - - - +
38B ARG* 2.8 71.4 + - + +
39B GLN* 5.9 0.2 - - - -
44B GLY 5.1 1.8 - - - +
45B LEU* 1.3 76.6 - - - +
47B TRP* 1.3 66.9 + - - +
48B VAL* 3.6 0.5 + - - +
61B ASN* 5.1 4.1 + - - +
63B LYS* 3.5 18.2 - - - +
64B PHE* 3.4 29.1 - - + -
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Residues in contact with TRP 47 (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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94A TYR* 4.0 15.3 - + + -
95A PRO* 3.7 22.4 - - + -
96A LEU* 3.4 56.5 + - + +
98A PHE* 4.2 11.3 - - + -
35B ASN* 2.7 23.2 + - - -
36B TRP 3.8 10.1 - - - -
37B VAL* 4.2 4.3 - - + -
46B GLU* 1.3 72.1 - - - +
48B VAL* 1.3 63.2 + - - +
49B GLY* 3.6 20.2 + - - -
50B MET* 3.6 27.6 - - + -
59B ARG* 3.7 17.0 - - - -
60B TYR 3.9 7.4 - - - -
61B ASN* 3.1 57.8 + - + +
64B PHE* 3.5 6.8 - - - -
108B PHE* 3.7 10.8 - + - -
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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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36B TRP* 2.9 27.4 + - + +
37B VAL 4.6 0.2 - - - -
38B ARG* 4.3 23.8 - - + +
46B GLU 4.0 8.3 - - - +
47B TRP* 1.3 75.0 - - - +
49B GLY* 1.3 59.7 + - - +
60B TYR* 4.0 7.7 - - + -
61B ASN* 3.1 22.9 + - - +
64B PHE* 3.9 24.7 - - + +
68B PHE* 3.7 27.6 - - + -
70B ILE* 4.3 7.6 - - + -
81B LEU* 4.3 14.6 - - + -
94B TYR* 4.8 7.6 - - + -
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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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35B ASN* 3.4 2.9 - - - -
36B TRP* 3.1 24.8 + - - -
47B TRP* 3.6 18.7 + - - -
48B VAL* 1.3 83.1 - - - +
50B MET* 1.3 60.4 + - - -
59B ARG 3.3 12.1 - - - -
60B TYR* 4.1 2.2 - - - -
70B ILE* 3.5 17.5 - - - +
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Residues in contact with MET 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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94A TYR* 3.6 29.6 - - + -
96A LEU* 4.5 1.6 - - + -
33B TRP* 3.7 29.2 - - + -
34B MET 3.2 9.0 - - - +
35B ASN* 3.3 27.8 - - - +
47B TRP* 3.6 12.6 - - + -
49B GLY* 1.3 72.5 - - - -
51B ILE* 1.3 59.6 + - - +
57B GLU 4.0 0.2 - - - +
58B THR* 3.3 5.0 - - - +
59B ARG* 2.8 55.3 + - + +
70B ILE* 4.0 5.6 - - - +
101B TYR* 4.5 2.7 - - - -
106B THR* 3.2 34.1 - - + +
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Residues in contact with ILE 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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33B TRP* 3.5 7.2 - - - -
34B MET* 2.8 37.7 + - + +
50B MET* 1.3 75.2 - - - +
52B HIS* 1.3 63.5 + - - +
53B PRO* 3.5 1.5 - - - +
56B SER* 3.7 30.3 - - - +
57B GLU 3.2 11.9 - - - +
58B THR* 3.6 17.3 - - + -
70B ILE* 3.7 9.9 - - + +
71B SER* 3.7 31.6 - - - -
72B VAL* 4.0 13.0 - - + +
79B LEU* 3.5 31.6 - - + -
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Residues in contact with HIS 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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30B THR 3.5 20.8 + - - -
31B GLY* 4.2 4.0 + - - -
32B HIS* 3.7 22.9 + - - -
33B TRP* 3.7 32.6 - + + -
51B ILE* 1.3 75.6 - - - +
53B PRO* 1.3 53.8 - - - +
54B SER* 2.6 36.7 + - - -
55B ASP* 3.4 1.2 + - - +
56B SER* 2.8 31.9 + - - -
57B GLU 2.8 12.1 + - - +
193J ASP 3.3 21.5 - - - -
197J LYS* 3.3 39.8 - - + +
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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