Contacts of the strand formed by residues 118 - 129 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASN* 5.2 2.2 - - - +
118A ARG* 6.6 0.4 - - - +
34D THR* 4.2 9.7 - - - +
45D TYR* 3.3 53.9 - - + -
47D ASN* 4.0 13.5 - - - +
116D GLY 3.9 1.2 + - - +
117D ASP* 1.3 71.7 - - - +
119D LEU* 1.3 56.4 + - - +
120D GLU* 3.0 50.5 + - - +
140D GLN 3.3 9.0 - - - +
141D VAL* 3.8 14.6 - - + +
142D ASP 4.7 3.1 + - - +
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Residues in contact with LEU 119 (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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45D TYR* 3.1 4.6 - - - -
46D LYS 2.9 46.2 + - - +
48D ILE* 4.0 13.5 - - + -
65D PHE* 3.9 27.4 - - + -
70D ILE* 3.9 14.6 - - + -
113D VAL* 3.9 24.9 - - + -
117D ASP 3.6 2.2 + - - -
118D ARG* 1.3 68.4 - - - +
120D GLU* 1.3 61.0 + - - +
121D TYR* 3.7 34.8 + - + +
139D ALA* 4.0 21.8 - - + -
140D GLN 3.8 1.3 - - - +
141D VAL* 4.1 7.9 - - + -
146D VAL* 4.0 7.2 - - + -
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Residues in contact with GLU 120 (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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34D THR* 5.0 1.4 + - - -
43D VAL* 4.0 12.4 - - + +
44D ALA 3.5 14.6 - - - +
45D TYR* 3.8 1.6 - - + -
118D ARG* 3.0 36.0 + - - +
119D LEU* 1.3 71.6 - - - +
121D TYR* 1.3 62.3 + - - +
122D HIS* 2.7 34.5 + - + +
139D ALA* 3.0 6.4 - - - -
140D GLN* 2.6 55.2 + - - +
143D GLY* 5.5 4.2 + - - -
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Residues in contact with TYR 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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29D LEU* 2.8 30.2 + - - +
30D VAL* 4.1 4.9 - - + -
42D ILE 3.5 1.6 - - - +
43D VAL* 3.1 9.4 - - - +
44D ALA* 2.7 34.5 + - + +
45D TYR* 4.0 13.7 - - - -
46D LYS* 3.5 25.5 - - + +
65D PHE* 5.0 0.3 - - - -
69D LEU 4.7 2.3 + - - -
70D ILE* 3.7 17.0 + - + -
73D GLY* 3.4 18.9 - - - -
74D MET* 3.7 17.5 - - + -
77D SER* 3.2 30.1 - - - +
119D LEU* 3.7 32.2 - - + +
120D GLU* 1.3 76.2 - - - +
122D HIS* 1.3 61.2 + - - +
123D LEU* 4.1 7.0 - - + -
138D THR 3.8 2.5 - - - -
139D ALA* 4.6 2.7 - - + -
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Residues in contact with HIS 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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41D LYS* 5.8 1.0 + - - -
42D ILE 3.8 2.9 - - - -
43D VAL* 3.7 28.6 - - + +
120D GLU* 2.7 38.1 + - + -
121D TYR* 1.3 76.1 - - - +
123D LEU* 1.3 63.0 + - - +
137D GLY* 3.2 6.2 - - - -
138D THR* 2.8 44.0 + - - +
140D GLN* 3.2 39.1 + - + +
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Residues in contact with LEU 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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41D LYS* 3.0 6.1 - - - +
42D ILE* 2.8 46.6 + - + +
74D MET* 2.8 56.1 - - + +
77D SER* 3.5 21.5 - - - -
78D GLY* 3.8 5.8 - - - +
81D LEU* 5.2 1.8 - - + -
121D TYR* 4.5 4.7 - - + -
122D HIS* 1.3 79.1 - - - +
124D GLU* 1.3 60.9 + - - +
135D VAL* 3.8 28.3 - - + -
136D GLY* 3.7 19.7 - - - +
137D GLY 4.0 0.2 - - - +
149D ALA 5.2 0.7 - - - +
151D LEU* 5.5 2.5 - - + -
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Residues in contact with GLU 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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40D GLN 3.1 11.4 - - - +
41D LYS* 4.0 7.0 - - + +
81D LEU* 5.3 0.2 - - - -
123D LEU* 1.3 75.6 - - - +
125D VAL* 1.3 68.0 + - - +
126D LEU* 3.4 20.0 + - + +
135D VAL* 3.3 6.6 - - - -
136D GLY 3.1 36.5 + - - +
137D GLY* 5.7 0.7 - - - -
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Residues in contact with VAL 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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39D ASN 3.5 30.3 - - - +
40D GLN* 2.7 11.8 + - - +
81D LEU* 3.7 21.1 - - + -
124D GLU* 1.3 78.1 - - - +
126D LEU* 1.3 63.9 + - - +
127D LYS* 3.6 21.5 - - - +
128D HIS* 3.8 28.9 - - + -
133D TRP* 3.7 19.5 - - + -
134D GLN 3.8 4.3 - - - +
135D VAL* 4.4 5.6 - - + -
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Residues in contact with LEU 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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124D GLU* 4.3 23.6 - - + +
125D VAL* 1.3 74.8 - - - +
127D LYS* 1.3 60.4 + - + +
134D GLN* 2.8 34.6 + - + +
135D VAL 3.8 21.1 - - - +
136D GLY* 3.8 15.5 - - - +
150D GLU* 4.0 25.6 - - + +
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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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125D VAL* 3.6 4.5 - - - +
126D LEU* 1.3 81.6 - - + +
128D HIS* 1.3 70.6 + - - +
129D LYS* 3.3 35.6 - - + +
132D ILE* 3.6 35.6 + - - +
134D GLN* 2.8 54.9 + - + +
152D LYS* 4.9 2.0 - - - +
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Residues in contact with HIS 128 (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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39D ASN* 3.6 35.7 + - + +
86D LEU* 5.0 5.5 - - + +
125D VAL* 3.8 15.5 - - + -
127D LYS* 1.3 84.5 - - - +
129D LYS* 1.3 69.9 + - - +
130D GLY 5.2 1.6 + - - -
132D ILE 3.3 7.6 - - - -
133D TRP* 3.5 43.9 + + + -
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Residues in contact with LYS 129 (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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127D LYS* 3.3 34.9 - - + +
128D HIS* 1.3 79.7 + - - +
130D GLY* 1.3 65.8 + - - +
131D MET 3.4 0.3 + - - -
132D ILE* 3.0 27.6 + - + +
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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