Contacts of the strand formed by residues 55 - 62 (chain B) in PDB entry 4Q29
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 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 6.1 2.2 - - + -
31A ASN* 4.6 13.1 - - + +
115A PHE* 4.1 10.8 - + - -
119A LEU* 3.0 36.1 - - + +
122A ASP* 5.3 2.1 + - - -
54B GLU* 1.3 76.8 - - - +
56B GLU* 1.3 57.6 + - - +
83B ILE* 6.3 3.1 - - + -
84B ILE 5.1 3.1 - - - -
86B LEU* 3.5 42.0 - - + +
106B TRP* 3.1 5.5 - - - +
107B TRP* 2.8 78.3 + + + +
108B ASP* 4.4 7.0 - - + -
109B LYS* 5.6 3.6 - - - -
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Residues in contact with GLU 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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52B HIS* 2.8 11.0 + - + -
54B GLU 4.0 3.6 - - - +
55B TYR* 1.3 78.0 - - - +
57B LEU* 1.3 64.3 + - - +
58B PHE* 3.8 16.5 - - + -
83B ILE* 3.8 5.7 - - - +
84B ILE* 3.1 37.0 + - + +
104B THR* 2.5 38.3 + - - +
105B ILE 3.2 7.6 - - - +
106B TRP* 4.2 15.2 - - + +
107B TRP* 3.9 5.0 - - - -
201B NI 2.3 41.7 - - + +
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Residues in contact with LEU 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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24A LEU* 4.1 26.2 - - + -
30A LEU* 4.9 0.2 - - + -
32A THR* 4.8 2.0 - - + -
34A PHE* 4.2 7.4 - - + -
103A TYR* 6.0 0.4 - - - +
105A ILE* 6.4 0.2 - - + -
56B GLU* 1.3 75.1 - - - +
58B PHE* 1.3 70.3 + - - +
59B ILE* 3.6 32.5 - - + -
81B LEU* 5.2 4.7 - - + -
82B ILE 3.1 13.7 - - - +
83B ILE* 3.5 24.2 - - + -
84B ILE* 4.6 0.7 - - - +
104B THR* 3.3 5.4 + - - -
105B ILE* 2.9 44.7 + - + +
107B TRP* 3.9 24.2 - - + -
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Residues in contact with PHE 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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56B GLU* 3.8 27.1 - - + -
57B LEU* 1.3 83.1 - - - +
59B ILE* 1.3 64.8 + - - +
60B VAL* 4.0 3.4 - - + -
67B ILE* 3.8 26.7 - - + -
80B ASP 3.9 0.7 - - - +
81B LEU* 3.4 8.7 - - - +
82B ILE* 2.8 49.2 + - + +
84B ILE* 4.3 13.9 - - + -
90B HIS* 4.2 22.7 - + + -
91B HIS* 5.5 1.3 - - - -
92B VAL* 3.9 23.6 - - + -
102B PHE* 3.7 35.7 - + + -
103B TYR 3.5 3.4 - - - -
104B THR* 3.9 4.3 - - - -
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Residues in contact with ILE 59 (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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38A TRP* 3.7 25.8 - - + -
59A ILE* 5.1 2.9 - - + -
61A ILE* 4.7 3.1 - - + -
103A TYR* 3.7 47.6 - - + -
105A ILE* 4.9 8.5 - - + -
57B LEU* 3.6 18.8 - - + -
58B PHE* 1.3 72.5 - - - +
60B VAL* 1.3 62.5 + - - +
61B ILE* 3.5 9.1 + - + +
81B LEU* 3.5 21.1 - - + -
102B PHE* 3.2 4.2 - - - -
103B TYR* 2.8 51.6 + - + +
105B ILE* 4.9 4.0 - - + -
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Residues in contact with VAL 60 (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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38A TRP* 3.3 9.2 - - - -
58B PHE* 4.9 4.9 - - + +
59B ILE* 1.3 72.4 - - - +
61B ILE* 1.3 61.2 + - - +
62B GLN 4.5 2.0 - - - +
63B GLY 4.8 0.4 - - - +
67B ILE* 5.0 1.8 - - + -
76B VAL* 3.9 19.7 - - + -
77B THR* 3.2 33.9 - - - +
78B LYS* 3.8 1.6 - - - +
79B GLY 2.9 24.9 + - - -
80B ASP* 2.9 25.9 + - + +
82B ILE* 4.8 10.8 - - + -
100B PHE* 3.5 32.3 - - + -
102B PHE* 4.1 6.5 - - + -
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Residues in contact with ILE 61 (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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38A TRP* 4.4 2.9 - - - -
59A ILE* 4.7 1.8 - - + -
61A ILE* 4.0 44.7 - - + +
62A GLN* 5.5 0.2 - - - +
78A LYS* 5.0 1.6 - - + -
38B TRP* 3.6 50.9 - - + -
59B ILE* 3.7 12.1 - - + +
60B VAL* 1.3 75.4 - - - +
62B GLN* 1.3 71.3 + - + +
78B LYS* 3.7 21.0 - - - +
101B HIS* 2.9 18.1 + - + +
102B PHE 4.1 1.1 - - - -
103B TYR* 3.9 28.5 - - + +
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Residues in contact with GLN 62 (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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61A ILE 6.0 0.2 - - - +
62A GLN* 6.1 0.9 - - - +
78A LYS* 3.7 25.8 - - + +
60B VAL* 3.9 1.2 - - - +
61B ILE* 1.3 91.1 - - + +
63B GLY* 1.3 76.7 + - - +
78B LYS* 4.8 7.9 - - + -
98B GLU* 5.4 7.3 + - - +
99B ASP* 4.3 4.9 + - - +
100B PHE* 3.3 11.0 - - - -
101B HIS* 2.9 50.3 + - + -
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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