Contacts of the strand formed by residues 134 - 146 (chain B) in PDB entry 1DS6
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 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B TYR* 3.1 6.9 - - - -
131B ARG 2.9 34.8 + - - +
132B THR* 4.2 9.2 - - - +
133B GLY* 1.3 82.5 - - - +
135B LYS* 1.3 64.3 + - - +
136B VAL* 3.4 12.4 + - + +
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Residues in contact with LYS 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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128B HIS* 3.9 44.3 + - + +
129B THR 3.5 10.5 - - - +
130B TYR* 3.5 26.2 + - + +
134B VAL* 1.3 75.1 - - - +
136B VAL* 1.3 62.0 + - - +
137B ASP 4.3 11.7 - - - +
138B LYS* 5.8 2.5 - - + -
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Residues in contact with VAL 136 (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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129B THR* 2.9 28.4 + - + +
131B ARG* 4.1 16.2 - - + -
134B VAL* 3.6 25.6 - - + +
135B LYS* 1.3 75.5 - - - +
137B ASP* 1.3 69.8 + - + +
172B TYR* 4.4 18.2 - - + -
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Residues in contact with ASP 137 (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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128B HIS* 3.6 2.9 - - - -
129B THR* 2.7 50.8 + - + +
135B LYS* 3.8 8.3 - - - +
136B VAL* 1.3 87.2 - - + +
138B LYS* 1.3 81.8 + - - +
139B ALA* 4.2 8.0 - - - +
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Residues in contact with LYS 138 (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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126B VAL* 4.0 8.6 - - + +
127B GLN 3.2 5.8 - - - +
128B HIS* 3.2 41.2 + - + +
129B THR* 6.0 0.2 - - - -
135B LYS* 5.8 3.6 - - + -
137B ASP* 1.3 86.7 + - - +
139B ALA* 1.3 69.3 + - - +
140B THR* 4.6 14.1 - - - -
177B PHE* 5.6 1.0 - - - -
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Residues in contact with ALA 139 (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 TYR* 4.7 2.5 - - + -
127B GLN* 2.8 47.3 + - + +
129B THR* 6.1 0.4 - - - +
137B ASP* 4.2 9.2 - - - +
138B LYS* 1.3 78.1 - - - +
140B THR* 1.3 66.7 + - - +
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Residues in contact with THR 140 (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 LYS* 4.2 19.4 + - - +
125B TYR* 3.1 17.7 - - - +
126B VAL* 3.8 24.0 - - + -
138B LYS* 4.6 14.1 - - - -
139B ALA* 1.3 84.0 - - - +
141B PHE* 1.3 70.6 + - - +
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Residues in contact with PHE 141 (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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72B LEU* 5.2 1.6 - - + -
109B VAL* 3.6 28.3 - - + -
111B ILE* 3.9 17.3 - - + -
124B LYS* 3.5 4.3 - - - -
125B TYR* 2.9 75.7 + + + -
140B THR* 1.3 81.7 - - - +
142B MET* 1.3 60.5 + - - +
143B VAL* 3.8 18.6 - - + -
155B PHE* 3.8 13.9 - + - -
157B THR* 3.6 29.4 - - + -
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Residues in contact with MET 142 (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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103A HIS* 3.3 50.5 - - + +
104A HIS* 3.4 29.5 - - - +
106A PRO* 4.6 15.4 - - + +
122B GLY* 3.6 25.8 - - - +
123B LEU 3.4 19.1 - - - +
124B LYS* 4.1 16.4 - - + +
141B PHE* 1.3 71.5 - - - +
143B VAL* 1.3 60.9 + - - +
144B GLY* 3.7 9.0 - - - +
155B PHE* 3.3 18.8 - - - -
181B ASP* 4.7 0.4 - - - +
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Residues in contact with VAL 143 (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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73A PRO* 4.8 2.6 - - - +
104A HIS 5.7 0.4 - - - -
111B ILE* 4.9 3.6 - - + -
113B PHE* 3.8 30.1 - - + -
123B LEU* 2.7 26.6 + - + +
124B LYS* 4.4 3.6 - - - -
141B PHE* 3.6 29.1 + - + +
142B MET* 1.3 74.1 - - - +
144B GLY* 1.3 58.5 + - - +
146B TYR* 2.8 33.8 + - + +
155B PHE* 3.6 26.6 - - + -
178B PHE* 4.4 18.4 - - + -
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Residues in contact with GLY 144 (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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73A PRO* 4.8 4.5 - - - -
104A HIS* 5.1 7.4 - - - -
120B VAL 4.0 0.7 - - - +
122B GLY 3.4 1.7 + - - -
123B LEU* 2.7 39.5 + - - +
142B MET* 3.5 15.2 - - - -
143B VAL* 1.3 80.3 - - - +
145B SER* 1.3 63.0 + - - -
146B TYR* 3.4 9.2 - - - -
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Residues in contact with SER 145 (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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66A ARG 5.2 1.3 + - - -
69A PRO* 3.9 17.3 + - - +
70A LEU* 3.5 36.0 - - - +
73A PRO* 3.8 12.3 - - - +
104A HIS* 3.4 20.2 + - - -
120B VAL 3.1 9.6 - - - -
121B SER* 3.6 8.1 + - - -
122B GLY 3.0 17.8 + - - -
144B GLY* 1.3 70.9 - - - -
146B TYR* 1.3 66.8 + - - +
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Residues in contact with TYR 146 (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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70A LEU* 4.2 7.6 - - - -
73A PRO* 3.8 27.4 - - + +
74A GLN* 4.8 4.9 + - - -
113B PHE* 3.8 23.1 - + - -
115B VAL* 3.8 21.5 - - + +
119B ILE* 3.5 3.6 - - - +
120B VAL* 3.0 32.1 + - + -
123B LEU* 5.1 4.0 - - + -
143B VAL* 2.8 40.0 + - + +
144B GLY* 3.4 18.4 - - - -
145B SER* 1.3 77.8 - - - +
147B GLY* 1.3 61.4 + - - +
153B TYR* 3.6 36.1 - + + -
154B GLU 4.8 3.7 + - - -
155B PHE* 3.8 15.2 - - - +
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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