Contacts of the strand formed by residues 53 - 58 (chain B) in PDB entry 3E5X
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 MET 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A PHE* 3.6 31.9 - - + -
52B SER* 1.3 72.1 - - - +
54B ILE* 1.3 60.0 + - - +
55B PHE 3.9 0.7 - - - -
83B LEU* 3.8 33.2 - - + -
84B ILE 3.2 9.9 - - - +
85B GLY* 4.3 5.8 - - - -
87B LEU* 3.9 15.2 - - + +
105B CYS 3.7 1.4 - - - +
106B TRP* 3.4 3.3 - - - -
107B PHE* 2.7 46.0 + - + +
112B LEU* 3.7 23.6 - - + -
126B ILE* 3.8 19.3 - - + -
130B TYR* 3.4 24.7 - - + +
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Residues in contact with ILE 54 (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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43B VAL* 4.5 3.1 - - + -
44B ILE* 4.2 19.7 - - + -
50B ILE* 4.0 15.9 - - + -
52B SER 3.9 4.5 - - - +
53B MET* 1.3 75.2 - - - +
55B PHE* 1.3 62.3 + - - +
56B LEU* 3.9 1.7 + - + +
61B ILE* 5.2 0.4 - - + -
82B SER 3.9 0.5 - - - +
83B LEU* 3.4 3.7 - - - -
84B ILE* 2.7 65.1 + - + +
104B THR* 3.8 32.5 - - + -
105B CYS 3.7 1.8 - - - -
106B TRP* 3.6 52.5 - - + +
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Residues in contact with PHE 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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22B ILE 3.3 26.7 - - - -
25B LEU* 3.7 23.6 - - + -
26B ARG* 3.8 29.8 - - + -
29B THR* 4.0 11.0 - - + -
53B MET 3.9 0.8 - - - -
54B ILE* 1.3 76.4 - - - +
56B LEU* 1.3 62.4 + - - +
57B VAL* 3.5 24.5 + - + -
81B ASN* 3.5 39.0 - - - -
82B SER 3.4 13.7 - - - -
83B LEU* 3.9 9.2 - - + -
104B THR* 3.1 5.7 - - - -
105B CYS* 2.8 44.5 + - + +
107B PHE* 3.8 13.7 - + + -
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Residues in contact with LEU 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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54B ILE* 3.9 2.2 + - + +
55B PHE* 1.3 73.9 - - - +
57B VAL* 1.3 59.2 + - - +
58B GLU 3.4 33.9 - - - +
59B GLY* 3.6 10.1 - - - +
60B LYS* 4.3 0.4 - - - -
61B ILE* 3.8 34.3 - - + +
78B ALA* 3.1 46.4 - - + +
79B GLY* 3.5 16.4 - - - +
81B ASN* 2.7 34.3 + - - -
82B SER* 2.9 16.0 + - - +
84B ILE* 6.0 2.5 - - + -
102B THR* 4.0 5.8 - - + -
103B ARG 3.9 2.2 - - - -
104B THR* 4.5 1.6 - - + +
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Residues in contact with VAL 57 (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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26B ARG* 2.5 50.1 + - + +
29B THR* 4.1 16.4 - - + -
34B ILE* 4.7 4.0 - - + -
55B PHE* 3.8 25.4 - - + -
56B LEU* 1.3 73.0 - - - +
58B GLU* 1.3 67.9 + - + +
80B GLY* 3.9 3.7 - - - -
103B ARG* 2.8 36.1 + - + +
104B THR 4.2 5.8 - - - +
105B CYS* 4.2 11.2 - - + -
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Residues in contact with GLU 58 (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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26B ARG* 5.0 1.8 - - - +
56B LEU* 3.4 9.1 - - - +
57B VAL* 1.3 85.8 - - + +
59B GLY* 1.3 59.6 + - - +
80B GLY* 4.4 5.6 - - - -
101B PRO 5.4 0.9 - - - +
102B THR* 3.2 2.3 - - - -
103B ARG* 2.8 34.9 + - + +
505B 3C4 3.7 30.7 - - - +
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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