Contacts of the strand formed by residues 121 - 126 (chain A) in PDB entry 3DH1
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A THR 4.3 0.4 + - - -
99A VAL* 3.4 30.5 - - + +
100A LEU 3.0 24.3 + - - -
119A ILE* 3.7 4.6 - - - +
120A PRO* 1.3 81.5 - - + +
122A VAL* 1.3 77.6 + - - +
123A VAL* 4.5 4.0 - - + -
153A GLN* 3.6 20.2 - - + +
155A ILE* 4.0 22.7 - - + -
121B LEU* 4.3 11.0 - - + -
153B GLN* 3.9 27.4 - - + -
154B CYS 5.3 0.4 - - - +
155B ILE* 4.3 22.9 - - + -
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Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 3.5 18.4 - - + +
102A VAL* 4.0 24.9 - - + -
106A PRO* 4.2 10.3 - - + -
114A LEU* 3.8 20.6 - - + -
119A ILE* 4.6 4.3 - - + -
121A LEU* 1.3 78.0 - - - +
123A VAL* 1.3 66.5 + - - +
124A TYR* 4.1 10.2 + - + -
152A PHE* 3.3 33.4 - - + -
153A GLN 2.9 10.3 + - - +
154A CYS* 3.2 8.6 - - - +
155A ILE 3.0 22.3 + - - -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.9 29.2 - - + +
26A MET* 3.7 23.4 - - + +
99A VAL* 4.7 1.8 - - + -
100A LEU 2.9 7.1 + - - +
101A TYR* 3.4 18.5 - - + -
102A VAL* 3.0 24.3 + - - +
121A LEU* 4.5 11.4 - - + -
122A VAL* 1.3 73.2 - - - +
124A TYR* 1.3 64.9 + - - +
155A ILE* 3.6 40.4 - - + +
158A TYR* 4.7 6.7 - - + -
19B MET* 4.9 0.9 - - + -
155B ILE* 5.5 1.6 - - + -
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Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 3.9 4.5 - - - -
102A VAL* 3.2 31.9 - - + +
104A VAL 4.4 1.3 - - - +
105A GLU* 3.5 43.1 - - + -
106A PRO* 4.1 11.0 - - + -
122A VAL* 4.2 9.4 - - + -
123A VAL* 1.3 71.2 - - - +
125A GLY* 1.3 67.7 + - - +
126A CYS 3.6 16.2 - - - -
127A GLN* 3.4 20.4 + - - -
134A CYS* 4.0 20.5 + - + +
154A CYS* 4.1 17.0 - - + -
155A ILE 3.1 8.9 + - - +
156A PRO* 3.3 31.3 - - + +
157A GLY 2.9 20.4 + - - -
158A TYR* 3.2 9.4 + - - +
16B PHE* 6.0 0.7 - - - -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 3.9 2.2 - - - +
102A VAL 3.1 9.6 + - - -
103A THR* 3.4 9.9 + - - -
124A TYR* 1.3 78.9 - - - +
126A CYS* 1.3 64.7 + - - +
127A GLN* 5.4 1.0 + - - -
157A GLY* 2.9 27.3 + - - -
158A TYR 3.4 20.9 - - - -
160A ALA* 3.8 7.4 - - - +
163A ALA* 4.8 1.6 - - - -
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Residues in contact with CYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A THR 3.4 7.5 + - - -
104A VAL* 4.1 5.4 - - - -
105A GLU 3.0 24.8 + - - -
124A TYR* 3.6 4.8 - - - -
125A GLY* 1.3 74.8 - - - -
127A GLN* 1.3 69.3 + - - +
160A ALA* 3.3 25.0 - - + +
163A ALA* 3.4 23.0 - - - +
164A VAL* 3.0 37.2 - - + -
167A LEU* 4.1 11.4 - - - -
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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