Contacts of the strand formed by residues 118 - 129 (chain B) in PDB entry 3DOY
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 ARG 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B THR* 3.9 13.3 - - - +
45B TYR* 3.5 65.2 + - + +
46B LYS 4.2 0.2 - - - -
47B ASN* 3.9 12.8 - - - +
116B GLY 4.0 1.2 + - - +
117B ASP* 1.3 74.2 - - - +
119B LEU* 1.3 57.7 + - - +
120B GLU* 3.3 27.0 + - + +
140B GLN 3.4 8.3 - - - +
141B VAL* 3.8 13.0 - - - +
142B ASP 4.5 3.3 + - - +
47F ASN* 5.3 1.3 - - - +
116F GLY 5.3 0.8 + - - -
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TYR* 3.0 4.5 - - - -
46B LYS 2.8 44.9 + - - +
48B ILE* 4.1 14.4 - - + -
65B PHE* 4.1 17.5 - - + -
70B ILE* 4.0 22.9 - - + -
113B VAL* 4.0 25.8 - - + -
117B ASP 3.7 2.4 + - - -
118B ARG* 1.3 68.0 - - - +
120B GLU* 1.3 60.6 + - - +
121B TYR* 3.8 34.6 + - + +
139B ALA* 4.1 11.9 - - + -
140B GLN 3.9 1.8 - - - +
141B VAL* 4.0 6.7 - - + -
146B VAL* 4.0 17.0 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 4.9 2.4 + - - +
43B VAL* 4.0 13.5 - - + +
44B ALA 3.3 11.4 - - - +
45B TYR* 3.8 10.8 - - + -
118B ARG* 3.3 26.5 + - + +
119B LEU* 1.3 72.4 - - - +
121B TYR* 1.3 62.3 + - - +
122B HIS* 2.8 32.2 + - - +
139B ALA* 3.3 4.5 - - - -
140B GLN* 2.7 52.8 + - - +
142B ASP 5.9 0.7 + - - -
143B GLY* 5.4 4.2 + - - -
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Residues in contact with TYR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 2.9 28.5 + - - +
30B VAL* 4.1 4.3 - - + -
42B ILE* 3.7 1.0 - - - +
43B VAL* 3.2 8.5 - - - +
44B ALA* 2.5 46.7 + - + +
45B TYR* 4.1 2.0 - - - -
46B LYS* 3.5 28.5 - - + +
65B PHE* 5.2 0.2 - - - -
69B LEU 4.6 2.3 + - - -
70B ILE* 3.7 11.9 - - + -
73B GLY* 3.5 25.7 - - - -
74B MET* 3.6 18.2 - - + -
77B SER* 3.1 27.8 - - - +
119B LEU* 3.8 27.5 - - + +
120B GLU* 1.3 74.9 - - - +
122B HIS* 1.3 62.6 + - - +
123B LEU* 3.9 12.3 - - + -
138B THR 3.8 3.4 - - - -
139B ALA* 4.9 2.5 - - + -
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Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 5.9 0.8 + - - -
42B ILE 3.7 4.3 - - - -
43B VAL* 3.6 28.7 - - + +
120B GLU* 2.8 42.0 + - - -
121B TYR* 1.3 77.6 - - - +
123B LEU* 1.3 61.7 + - - +
137B GLY* 3.0 6.9 - - - -
138B THR* 2.8 44.6 + - - +
140B GLN* 3.3 35.7 + - + +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS* 3.3 4.3 - - - +
42B ILE* 2.9 47.4 + - + +
74B MET* 3.7 46.7 - - + +
77B SER* 4.2 4.5 - - - -
78B GLY* 4.3 6.7 - - - +
81B LEU* 4.6 1.6 - - + -
121B TYR* 3.9 16.2 - - + -
122B HIS* 1.3 88.3 - - - +
124B GLU* 1.3 61.1 + - - +
135B VAL* 3.9 24.2 - - + -
136B GLY* 3.4 23.3 - - - -
137B GLY 3.9 2.5 - - - +
151B LEU* 4.3 6.7 - - + -
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLN* 3.2 19.5 + - - +
41B LYS* 4.0 7.6 - - + +
81B LEU* 4.6 0.4 - - - -
123B LEU* 1.3 75.5 - - - +
125B VAL* 1.3 67.2 + - - +
126B LEU* 3.4 20.0 + - + +
135B VAL* 3.2 6.9 - - - -
136B GLY 2.9 39.7 + - - +
137B GLY* 5.5 2.4 - - - -
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN 3.5 31.6 - - - +
40B GLN* 2.9 17.9 + - - +
81B LEU* 3.7 23.6 - - + -
124B GLU* 1.3 75.5 - - - +
126B LEU* 1.3 64.3 + - - +
127B LYS* 3.8 14.6 - - - +
128B HIS* 3.8 28.7 - - + -
133B TRP* 3.8 25.4 - - + -
134B GLN 3.7 4.9 - - - +
135B VAL* 4.3 3.8 - - + -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLU* 4.1 26.0 - - + +
125B VAL* 1.3 74.9 - - - +
127B LYS* 1.3 66.7 + - + +
134B GLN* 2.7 27.0 + - + +
135B VAL 3.8 11.9 - - - +
136B GLY* 3.9 11.7 - - - +
150B GLU* 3.8 39.3 - - + +
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL* 3.4 6.5 - - - +
126B LEU* 1.3 83.4 - - + +
128B HIS* 1.3 67.6 + - - +
129B LYS* 5.8 5.4 - - - +
133B TRP* 3.8 0.2 - - - -
134B GLN* 2.8 73.3 + - + +
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Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN* 3.1 32.0 + - - +
125B VAL* 3.8 18.4 - - + -
127B LYS* 1.3 83.3 - - - +
129B LYS* 1.3 65.9 + - - +
130B GLY 5.1 2.4 + - - -
132B ILE 3.3 5.8 - - - -
133B TRP* 3.4 48.1 + + + -
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LYS* 5.8 5.8 - - - +
128B HIS* 1.3 77.5 - - - +
130B GLY* 1.3 67.3 + - - +
131B MET 3.3 0.5 + - - -
132B ILE* 3.0 28.5 + - + +
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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