Contacts of the strand formed by residues 125 - 131 (chain D) in PDB entry 3CB4
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 GLU 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D GLU 3.1 9.6 + - - +
97D GLY* 3.2 1.6 - - - -
98D ALA 2.8 26.4 + - - +
124D LEU* 1.3 68.1 - - - +
126D VAL* 1.3 67.4 + - - +
127D VAL* 3.5 2.6 + - + +
179D ASP* 3.3 38.2 - - - +
180D ILE* 3.9 19.7 - - + +
181D PRO* 4.0 9.9 - - + -
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Residues in contact with VAL 126 (chain D).
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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10D ILE* 5.8 1.6 - - + -
98D ALA* 3.4 13.5 - - + +
100D LEU* 3.9 27.1 - - + +
116D CYS* 4.3 14.4 - - - +
119D ALA* 4.3 17.5 - - + -
120D MET* 3.8 27.1 - - + -
124D LEU* 3.3 9.0 + - + +
125D GLU* 1.3 78.3 + - - +
127D VAL* 1.3 63.1 + - - +
128D PRO* 3.4 11.4 - - - +
153D ILE* 4.3 25.7 - - + +
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Residues in contact with VAL 127 (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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98D ALA 2.7 9.6 + - - +
99D LEU* 3.4 22.6 - - + -
100D LEU 2.8 24.7 + - - -
125D GLU* 4.0 2.9 - - + +
126D VAL* 1.3 74.1 - - - +
128D PRO* 1.3 75.9 - - + +
129D VAL* 3.5 8.8 + - + +
159D VAL* 5.8 1.3 - - + -
172D VAL* 5.2 2.2 - - - +
175D ARG* 4.0 27.4 - - + +
176D LEU* 4.6 9.2 - - - +
179D ASP* 4.7 13.9 - - + +
180D ILE* 4.0 33.7 - - + -
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Residues in contact with PRO 128 (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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100D LEU* 3.7 10.8 - - + +
126D VAL* 3.4 10.7 - - - +
127D VAL* 1.3 89.1 - - + +
129D VAL* 1.3 64.8 + - - +
147D ILE* 4.5 16.8 - - + -
153D ILE* 4.0 18.4 - - + -
154D ASP 3.6 22.2 - - - +
155D ALA* 4.3 3.1 - - + -
158D ALA* 3.6 32.6 - - + +
159D VAL* 3.9 6.8 + - - +
175D ARG* 5.7 2.8 + - - +
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Residues in contact with VAL 129 (chain D).
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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20D LEU* 4.2 12.1 - - + -
99D LEU* 4.7 9.6 - - + -
100D LEU 2.7 13.0 + - - +
101D VAL* 3.5 11.4 - - + -
102D VAL* 2.8 30.8 + - - +
127D VAL* 4.0 16.6 - - + +
128D PRO* 1.3 78.8 - - - +
130D LEU* 1.3 66.2 + - - +
131D ASN 3.5 0.2 + - - -
147D ILE* 5.6 1.7 - - - +
159D VAL* 3.7 7.6 - - + +
161D CYS* 3.8 28.3 - - - -
172D VAL* 3.8 33.4 - - + -
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Residues in contact with LEU 130 (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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102D VAL 3.6 4.3 - - - +
104D ALA* 4.9 4.9 - - + -
129D VAL* 1.3 70.5 - - - +
131D ASN* 1.3 61.4 + - - +
133D ILE* 4.5 7.4 - - + +
140D PRO* 4.2 19.5 - - + +
143D VAL* 3.8 20.0 - - + -
144D ALA* 4.3 8.1 - - + +
147D ILE* 3.8 28.5 - - + -
155D ALA 5.3 0.2 - - - +
158D ALA* 4.1 22.4 - - + +
159D VAL 3.0 10.2 + - - +
160D ARG* 3.3 45.1 - - + +
161D CYS* 3.0 27.7 + - - +
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Residues in contact with ASN 131 (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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20D LEU* 4.1 5.2 + - - +
23D ARG* 2.6 44.3 + - - +
101D VAL* 3.7 28.5 - - + +
102D VAL 2.7 19.5 + - - +
103D ASP* 3.7 2.0 - - - +
104D ALA* 2.9 27.4 + - - +
129D VAL* 3.5 0.6 + - + -
130D LEU* 1.3 71.7 - - - +
132D LYS* 1.3 88.6 + - + +
133D ILE 3.4 1.8 - - - -
161D CYS* 3.3 19.0 + - - -
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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