Contacts of the strand formed by residues 120 - 127 (chain D) in PDB entry 6DBV
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 VAL 120 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D ASP* 5.1 11.2 - - + +
29D TYR* 3.1 35.2 - - + +
58D ARG* 6.3 2.7 - - - -
60D ILE* 5.0 9.7 - - + +
61D SER* 2.8 23.9 + - - -
111D VAL* 4.5 0.9 - - + -
113D SER 4.2 2.0 - - - -
114D ARG* 3.2 29.4 - - - +
118D ARG 4.3 7.4 - - - +
119D LYS* 1.3 84.6 - - - +
121D THR* 1.3 69.5 + - - +
122D LEU* 4.2 13.2 - - + -
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Residues in contact with THR 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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61D SER* 4.1 9.6 - - - +
62D PHE 5.7 4.3 - - - -
63D SER* 5.8 1.8 - - - -
111D VAL* 3.5 3.5 - - - +
112D ASP* 2.9 23.2 + - - +
113D SER* 2.6 56.1 + - - +
115D GLY 4.2 11.4 - - - +
119D LYS* 5.2 6.3 - - + -
120D VAL* 1.3 82.7 - - - +
122D LEU* 1.3 71.0 + - - +
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Residues in contact with LEU 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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24D LEU* 4.7 1.8 - - + -
29D TYR* 4.3 27.6 - - + +
45D ILE* 5.0 5.2 - - + -
60D ILE* 3.6 29.4 - - + -
61D SER 3.9 6.4 + - - +
62D PHE* 3.1 27.9 - - + +
63D SER* 3.1 19.8 + - - -
109D LEU* 3.8 20.2 - - + -
110D SER 3.2 10.8 - - - +
111D VAL* 3.6 25.8 - - + +
112D ASP* 4.3 4.3 - - - +
120D VAL* 4.2 11.7 - - + -
121D THR* 1.3 85.2 - - - +
123D ARG* 1.3 63.9 + - - +
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Residues in contact with ARG 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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62D PHE* 3.6 6.7 - - - -
63D SER* 4.1 9.7 + - - +
65D ASN* 2.8 50.4 + - - +
66D SER* 3.7 12.8 - - - +
86D LYS* 3.4 27.9 - - - +
108D MET 3.9 0.3 - - - +
109D LEU* 3.4 4.5 - - - +
110D SER* 2.9 37.5 + - - +
111D VAL 6.2 0.2 - - - -
112D ASP* 5.4 16.0 + - + -
122D LEU* 1.3 76.9 - - - +
124D CYS* 1.3 65.1 + - - +
125D GLU* 2.8 36.1 + - + +
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Residues in contact with CYS 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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31D PHE* 6.2 0.7 - - - -
45D ILE* 4.8 2.7 - - - -
62D PHE* 3.4 30.7 - - + -
65D ASN 4.9 0.2 - - - +
66D SER* 3.8 6.4 - - - -
67D SER* 2.3 56.1 + - - +
69D LEU* 5.1 23.1 - - + -
92D ILE* 6.3 0.2 - - - -
107D TYR* 5.5 3.6 - - + -
108D MET 3.4 7.0 - - - +
109D LEU* 3.5 28.7 - - - -
123D ARG* 1.3 72.7 - - - +
125D GLU* 1.3 57.9 + - - +
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Residues in contact with GLU 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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65D ASN 5.4 3.9 - - - +
67D SER* 3.8 1.1 - - - -
86D LYS* 4.0 9.9 + - - +
107D TYR* 4.6 1.8 - - - -
108D MET* 2.9 58.3 + - + +
123D ARG* 2.8 50.9 + - + +
124D CYS* 1.3 72.6 - - - +
126D GLU* 1.3 68.1 + - - +
127D LYS* 3.7 2.8 + - - +
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Residues in contact with GLU 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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67D SER* 3.3 17.5 + - - +
105D SER* 5.1 7.7 - - - -
106D LEU 3.9 2.0 - - - +
107D TYR* 3.5 37.4 - - + +
125D GLU* 1.3 77.3 - - - +
127D LYS* 1.3 68.2 + - - +
128D GLU* 2.7 35.5 + - - +
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Residues in contact with LYS 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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105D SER* 5.6 0.3 - - - -
106D LEU* 3.0 46.8 + - + +
107D TYR* 5.8 0.2 - - - -
108D MET* 3.0 36.7 - - + +
125D GLU* 3.7 4.1 + - - +
126D GLU* 1.3 82.2 - - - +
128D GLU* 1.3 69.5 + - - +
129D LEU* 3.6 12.7 + - + +
187D LEU* 3.1 46.7 - - + +
188D GLU* 5.3 5.4 - - - -
190D GLY* 6.2 0.9 - - - -
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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