Contacts of the strand formed by residues 119 - 123 (chain D) in PDB entry 3DBL
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 ASN 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D ARG* 3.1 29.7 + - + +
74D GLN* 3.6 22.3 - - - +
75D ILE 3.3 9.4 + - - +
112D ASN* 3.5 2.3 - - - -
117D ASN 3.5 6.0 + - - +
118D CYS* 1.3 74.1 - - - +
120D VAL* 1.3 61.6 + - - +
121D VAL* 3.5 16.5 + - - +
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LEU* 4.2 7.9 - - + -
75D ILE* 2.9 18.8 - - + +
77D VAL* 3.5 32.1 - - + -
108D ALA* 3.5 23.2 - - + +
111D LEU* 4.0 18.4 - - + -
112D ASN* 2.8 29.6 + - - +
118D CYS* 3.6 25.4 - - - -
119D ASN* 1.3 70.9 - - - +
121D VAL* 1.3 64.3 + - - +
122D PRO* 3.4 9.4 - - - +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE* 3.5 42.2 - - + -
75D ILE 2.7 12.3 + - - +
76D HIS* 3.4 20.9 - - + +
77D VAL 2.9 26.0 + - - +
119D ASN* 3.9 21.3 - - - +
120D VAL* 1.3 75.9 - - - +
122D PRO* 1.3 68.0 - - + +
123D HIS* 3.8 24.6 - - + +
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Residues in contact with PRO 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLU* 4.7 15.9 - - - +
122B PRO* 5.7 1.9 - - + +
123B HIS* 6.1 0.3 - - - -
124B PHE* 5.6 3.8 + - - +
77D VAL* 3.7 5.8 - - + +
104D ALA* 3.0 34.1 - - + +
105D GLU* 3.9 13.2 - - + +
108D ALA* 3.8 11.4 - - + -
120D VAL 3.4 10.1 - - - +
121D VAL* 1.3 89.0 - - + +
123D HIS* 1.3 69.1 + - - +
124D PHE 4.0 1.5 + - - +
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Residues in contact with HIS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B HIS* 5.7 1.5 + - - -
124B PHE* 4.0 11.3 + - + -
125B ASN* 3.6 36.3 + - - -
76D HIS* 3.1 31.6 + + + -
77D VAL 2.8 21.0 + - - +
78D ILE* 3.5 16.9 - - + -
79D ASP 3.3 20.1 + - - +
104D ALA* 3.7 4.5 - - - +
121D VAL* 3.8 24.6 - - + +
122D PRO* 1.3 74.1 + - - +
124D PHE* 1.3 60.2 + - - +
125D ASN* 2.8 19.9 + - - +
130D PHE* 4.4 5.9 - + + -
134D PHE* 3.9 17.8 - + - -
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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