Contacts of the strand formed by residues 124 - 135 (chain B) in PDB entry 4DQ0
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 THR 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLU* 5.4 0.4 - - - -
96B TYR 3.5 9.4 - - - +
99B ILE* 3.5 6.0 - - + +
120B MET 2.7 22.0 + - - -
121B GLN 3.8 6.7 - - - -
122B ARG 3.3 2.5 - - - +
123B CYS* 1.3 79.7 - - - +
125B LYS* 1.3 73.5 + - - +
126B PRO* 3.9 1.2 - - - +
128B GLY 3.6 24.0 - - - -
129B TYR 3.8 2.5 - - - +
130B ASN* 2.9 26.6 + - - +
163B TRP* 3.8 14.8 - - + -
196B LYS* 3.0 25.6 + - + +
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLU* 3.8 44.6 + - + +
96B TYR 2.9 19.8 + - - +
97B ASP* 3.5 24.7 + - - +
124B THR* 1.3 78.4 - - - +
126B PRO* 1.4 74.1 - - + +
127B GLY 3.3 0.3 + - - -
128B GLY* 2.7 27.6 + - - +
196B LYS* 3.7 4.7 - - - +
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Residues in contact with PRO 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 THR 4.3 2.2 - - - +
125B LYS* 1.4 94.8 - - + +
127B GLY* 1.3 60.6 + - - +
128B GLY 3.4 0.2 + - - -
196B LYS* 4.2 7.6 - - + +
197B LYS 3.5 22.9 - - - +
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Residues in contact with GLY 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 LYS 3.3 0.2 + - - -
126B PRO* 1.3 71.4 - - - +
128B GLY* 1.3 61.6 + - - +
129B TYR* 3.5 8.1 - - - -
195B ARG* 2.9 38.8 + - - -
196B LYS 2.7 22.0 + - - -
197B LYS 4.2 1.4 + - - -
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Residues in contact with GLY 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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97B ASP* 3.3 19.5 - - - -
124B THR* 3.6 11.0 - - - +
125B LYS* 2.7 24.5 + - - +
126B PRO 3.2 1.6 + - - -
127B GLY* 1.3 72.6 - - - +
129B TYR* 1.3 63.1 + - - -
195B ARG* 3.4 3.1 - - - -
196B LYS 2.9 25.1 + - - -
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Residues in contact with TYR 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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28B VAL* 3.9 28.2 + - + +
29B VAL* 3.7 37.9 - - + -
30B LYS 5.6 0.2 - - - -
97B ASP 2.7 13.8 + - - -
98B PHE* 3.3 18.2 + - + -
99B ILE 2.8 21.4 + - - -
124B THR* 3.8 1.7 - - - +
127B GLY 3.5 15.9 - - - -
128B GLY* 1.3 77.7 - - - -
130B ASN* 1.3 73.8 + - - +
166B VAL* 4.2 10.5 - - + -
193B LEU* 4.0 16.6 - - + -
194B ALA 3.3 7.6 - - - +
195B ARG* 3.2 48.3 + - + -
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Residues in contact with ASN 130 (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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99B ILE* 3.3 15.6 - - - +
120B MET* 3.9 23.7 - - + +
124B THR* 2.9 26.3 + - - +
129B TYR* 1.3 87.0 + - - +
131B LEU* 1.3 59.0 + - - +
132B ILE* 4.1 0.4 - - + -
160B TYR* 2.8 42.2 + - + +
163B TRP* 3.5 14.2 - - + -
192B MET* 3.5 6.0 - - + +
193B LEU* 3.4 4.5 - - - +
194B ALA* 2.8 36.6 + - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLU* 4.0 33.9 - - + +
22B VAL* 3.7 34.3 - - + +
25B ALA* 4.6 1.6 - - + -
98B PHE* 3.8 23.0 - - + -
99B ILE 2.9 8.7 + - - +
100B LEU* 3.4 9.9 - - + -
101B SER 2.8 27.5 + - - -
102B THR* 4.1 15.0 - - + -
120B MET* 5.0 0.3 - - - +
130B ASN* 1.3 71.6 - - - +
132B ILE* 1.3 67.9 + - - +
133B VAL* 4.4 7.6 - - + -
167B LYS* 6.1 1.1 - - + -
191B THR* 5.3 1.3 - - + -
192B MET 3.2 19.1 - - - +
193B LEU* 4.1 14.4 - - + +
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Residues in contact with ILE 132 (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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101B SER* 3.5 11.7 - - - +
105B LEU* 3.9 27.4 - - + -
117B ILE* 4.9 3.6 - - + -
120B MET* 3.9 22.7 - - + -
130B ASN* 4.1 0.6 - - + -
131B LEU* 1.3 81.6 - - - +
133B VAL* 1.3 75.9 + - - +
151B PHE* 4.3 5.2 - - + -
156B LEU* 4.0 25.7 - - + +
160B TYR* 3.5 39.3 - - + +
190B ALA 3.6 0.9 - - - +
191B THR* 3.5 1.9 - - - -
192B MET* 2.8 46.4 + - + +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B HIS* 4.2 20.0 - - + +
21B GLU* 4.1 27.6 - - + -
101B SER 3.1 8.3 + - - +
102B THR* 4.3 10.3 - - + -
103B VAL* 2.8 47.7 + - + +
104B VAL 4.5 1.0 + - - -
105B LEU* 5.3 0.9 + - - +
131B LEU* 4.4 7.0 - - + -
132B ILE* 1.3 81.7 - - - +
134B ALA* 1.3 65.2 + - - +
189B PHE* 4.8 11.0 - - + -
190B ALA 3.2 4.3 - - - +
191B THR* 4.0 16.8 - - + +
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Residues in contact with ALA 134 (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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105B LEU* 4.3 14.4 - - + -
106B MET* 3.8 16.2 - - + +
132B ILE* 4.6 2.4 - - + +
133B VAL* 1.3 78.1 - - - +
135B ALA* 1.3 64.2 + - - +
149B PHE* 5.6 1.1 - - + -
151B PHE* 3.6 33.4 - - + -
189B PHE* 3.4 7.7 - - - -
190B ALA* 2.9 34.3 + - - +
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Residues in contact with ALA 135 (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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106B MET* 3.4 26.2 - - + +
134B ALA* 1.3 79.2 - - - +
136B MET* 1.3 61.9 + - - +
147B PHE* 3.6 35.4 - - + -
149B PHE 4.9 0.2 - - - +
150B ALA* 3.6 6.5 - - + -
151B PHE* 3.1 20.1 + - - +
187B LEU* 4.0 11.4 - - + -
188B ARG 4.1 0.2 - - - -
189B PHE* 3.8 12.1 - - + -
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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