Contacts of the strand formed by residues 133 - 138 (chain D) in PDB entry 6D6U
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 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D ASP* 2.8 24.1 - - - +
64D VAL* 3.4 26.7 + - + +
66D PHE* 4.4 12.3 - - + -
101D PHE* 3.9 33.2 - - + -
107D SER* 5.9 0.9 - - - -
108D VAL 3.7 5.6 - - - +
109D ALA* 3.8 13.5 - - + -
131D MET* 3.7 33.1 - - + -
132D ARG* 1.3 77.5 - - - +
134D THR* 1.3 64.4 + - - +
135D VAL* 4.0 5.8 - - + -
124E ILE* 3.6 24.9 - - + +
125E THR* 4.3 12.1 - - - +
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Residues in contact with THR 134 (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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102C LYS* 5.9 2.9 - - - +
61D THR* 4.1 23.1 - - + -
62D ILE 3.7 5.6 - - - +
63D ASP* 4.7 7.8 + - + +
106D LYS 4.6 1.2 - - - +
107D SER* 3.7 2.6 - - - -
108D VAL* 2.9 48.0 + - + +
110D HIS* 2.6 32.9 + - + -
133D LEU* 1.3 73.7 + - - +
135D VAL* 1.3 60.9 - - - +
136D ARG* 3.8 9.6 + - - +
187D ARG* 5.8 4.0 - - - +
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Residues in contact with VAL 135 (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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61D THR* 3.5 5.0 - - - +
62D ILE* 2.8 52.8 + - + +
64D VAL* 3.9 24.7 - - + -
101D PHE* 3.3 44.6 - - + -
104D GLY* 5.3 1.6 - - - -
107D SER* 3.8 10.1 - - - +
133D LEU* 4.0 7.0 - - + -
134D THR* 1.3 75.4 - - - +
136D ARG* 1.3 62.7 + - - +
137D ALA* 3.9 10.3 - - + +
155D LEU* 4.2 14.6 - - + -
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Residues in contact with ARG 136 (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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59D GLU* 3.3 42.7 + - + +
60D TYR 3.8 4.7 - - - +
61D THR* 3.9 21.5 + - - +
104D GLY* 3.6 2.8 - - - -
105D LYS* 2.9 25.1 + - - +
106D LYS* 2.4 70.5 + - - +
107D SER* 3.9 7.1 + - - +
108D VAL* 4.8 13.9 - - - +
134D THR* 3.8 12.4 + - - +
135D VAL* 1.3 76.7 - - - +
137D ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 137 (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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59D GLU* 3.3 23.9 - - - +
60D TYR* 3.3 43.5 + - + +
62D ILE* 5.6 0.2 - - + -
103D ASN* 3.3 17.7 - - - +
104D GLY* 3.8 2.9 - - - -
105D LYS* 4.2 2.1 - - - -
135D VAL* 3.9 5.0 - - + -
136D ARG* 1.3 78.8 - - - +
138D GLU* 1.3 61.9 + - - +
154D PRO 4.5 0.9 - - - +
155D LEU* 4.0 19.1 - - + -
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Residues in contact with GLU 138 (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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57D ASP 5.5 1.1 - - - +
58D MET* 3.8 15.2 - - + +
60D TYR* 4.5 1.3 - - - -
103D ASN* 3.0 37.4 + - + +
105D LYS* 4.2 28.7 - - + +
137D ALA* 1.3 78.4 - - - +
139D CYS* 1.3 67.4 + - - +
140D PRO* 4.2 6.7 - - + +
154D PRO* 4.6 2.6 - - - +
61E SER* 4.5 15.9 + - - -
195E SER 4.6 8.9 - - - +
197E ARG* 4.2 24.1 - - - +
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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