Contacts of the strand formed by residues 121 - 126 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D THR 4.2 0.2 + - - -
99D VAL* 3.5 32.1 - - + -
100D LEU 3.0 22.2 + - - -
119D ILE* 3.3 10.1 - - - +
120D PRO* 1.3 86.6 - - + +
122D VAL* 1.3 79.1 + - - +
123D VAL* 4.7 3.4 - - + -
153D GLN* 3.6 24.7 - - + +
155D ILE* 4.2 28.3 - - + -
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Residues in contact with VAL 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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100D LEU* 3.3 17.0 - - + +
102D VAL* 4.1 22.2 - - + -
106D PRO* 4.3 11.2 - - + -
114D LEU* 4.0 17.3 - - + -
119D ILE* 4.2 9.4 - - + -
121D LEU* 1.3 81.1 - - - +
123D VAL* 1.3 66.8 + - - +
124D TYR* 4.0 10.8 + - + -
152D PHE* 3.6 30.5 - - + -
153D GLN 3.0 9.4 + - - +
154D CYS* 3.3 7.0 - - - +
155D ILE 3.0 23.7 + - - -
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Residues in contact with VAL 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D THR* 4.1 21.8 - - + -
26D MET* 3.4 30.3 - - + +
99D VAL* 4.7 7.4 - - + -
100D LEU 2.6 13.3 + - - +
101D TYR* 3.2 14.5 - - + -
102D VAL 2.9 24.4 + - - -
121D LEU* 4.7 4.7 - - + -
122D VAL* 1.3 77.9 - - - +
124D TYR* 1.3 60.6 + - - +
155D ILE* 3.7 36.6 - - + +
158D TYR* 4.7 6.5 - - + -
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Residues in contact with TYR 124 (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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26D MET* 3.7 6.1 - - - +
102D VAL* 3.1 28.7 - - + +
105D GLU* 3.6 23.3 - - + +
106D PRO* 4.1 11.4 - - + -
122D VAL* 4.4 9.4 - - + -
123D VAL* 1.3 74.0 - - - +
125D GLY* 1.3 65.7 + - - +
126D CYS 3.5 24.5 - - - -
127D GLN* 3.3 26.7 + - - -
134D CYS* 4.0 28.2 + - + +
154D CYS* 4.1 15.5 - - + -
155D ILE 3.4 6.6 + - - +
156D PRO* 3.4 31.2 - - + +
157D GLY 3.1 18.9 + - - -
158D TYR* 3.3 7.4 + - - +
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Residues in contact with GLY 125 (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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26D MET* 3.8 2.4 - - - +
102D VAL 3.3 7.7 + - - -
103D THR* 3.4 9.6 + - - -
124D TYR* 1.3 77.5 - - - +
126D CYS* 1.3 61.5 + - - +
127D GLN* 5.4 1.2 + - - -
157D GLY* 2.8 30.1 + - - -
158D TYR 3.3 22.0 - - - -
160D ALA* 3.7 8.8 - - - +
163D ALA* 4.9 2.2 - - - -
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Residues in contact with CYS 126 (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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103D THR 3.2 11.3 + - - -
104D VAL* 3.9 15.9 - - - -
105D GLU 2.9 26.2 + - - -
124D TYR* 3.5 6.4 - - - -
125D GLY* 1.3 74.6 - - - +
127D GLN* 1.3 71.0 + - - +
160D ALA* 3.5 31.3 - - + +
163D ALA* 3.5 20.6 - - + +
164D VAL* 3.7 21.3 - - + +
167D LEU* 4.1 6.3 - - - -
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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