Contacts of the strand formed by residues 140 - 153 (chain B) in PDB entry 1AOC
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 CYS 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B CYS* 2.0 55.2 - - + -
89B PRO* 5.1 1.8 - - - -
127B CYS* 4.2 3.0 - - - -
129B PHE 3.8 15.0 - - - +
130B GLY 4.2 0.2 - - - -
131B SER* 2.9 36.1 + - - +
132B ASN* 3.0 33.5 + - - +
134B CYS* 3.5 8.2 - - - -
139B ARG* 1.3 75.0 + - - +
141B THR* 1.3 60.1 + - - +
170B CYS* 3.8 4.7 - - - -
171B PRO 3.8 1.8 - - - -
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Residues in contact with THR 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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127B CYS* 3.5 3.1 - - - -
139B ARG* 2.7 44.4 + - - +
140B CYS* 1.3 71.9 - - - +
142B GLN* 1.3 67.9 + - - +
170B CYS* 3.1 5.6 - - - -
171B PRO* 3.0 36.4 + - - +
173B ARG* 3.3 27.7 - - + +
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Residues in contact with GLN 142 (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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6B PRO* 3.4 41.5 - - + +
125B HIS 2.9 18.5 + - - -
126B LYS* 3.1 5.5 - - - -
127B CYS* 3.0 32.6 + - - -
139B ARG* 4.4 3.6 - - - +
140B CYS 4.2 0.2 + - - -
141B THR* 1.3 80.4 - - - +
143B GLN* 1.3 72.1 + - - +
144B ARG* 3.8 11.5 + - + +
167B CYS* 3.4 23.8 - - - +
169B GLY 2.6 25.8 + - - -
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Residues in contact with GLN 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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75B CYS* 3.1 28.7 - - + -
84B PHE* 4.0 6.5 - - + -
141B THR 3.2 1.6 + - - -
142B GLN* 1.3 79.0 + - - +
144B ARG* 1.3 81.5 + - - +
167B CYS* 3.7 0.2 - - - -
168B CYS* 3.0 27.3 + - - -
169B GLY 2.7 17.0 + - - +
171B PRO* 3.5 17.8 - - + +
173B ARG* 3.6 22.5 + - - -
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Residues in contact with ARG 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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6B PRO* 5.9 1.3 - - - -
7B ILE* 3.2 41.4 + - - +
8B CYS* 5.0 2.6 - - - +
142B GLN* 3.8 12.4 + - + +
143B GLN* 1.3 99.1 + - - +
145B SER* 1.3 65.2 + - - +
165B ARG* 3.5 54.3 + - + +
166B THR 3.1 7.4 - - - +
167B CYS* 3.9 19.1 - - - -
168B CYS* 4.0 1.3 - - - -
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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
----------------------------------------------------------
78B PHE* 3.0 46.4 - - - +
79B PRO 5.2 1.4 + - - -
144B ARG* 1.3 75.6 - - - +
146B VAL* 1.3 68.6 + - - +
165B ARG* 3.0 10.1 - - - +
166B THR* 2.7 36.4 + - - -
168B CYS* 3.9 11.9 - - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 3.4 19.1 - - - -
103B VAL* 3.9 19.3 - - + -
145B SER* 1.3 84.2 + - - +
147B VAL* 1.3 65.7 - - - +
148B ARG* 5.1 3.4 - - + -
163B SER* 3.7 31.4 - - - +
164B PHE 3.3 5.6 - - - +
165B ARG* 4.8 11.0 - - + +
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Residues in contact with VAL 147 (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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9B LEU* 4.5 4.9 - - + -
63B TYR* 3.4 47.1 - - + +
78B PHE* 4.3 4.9 - - + -
122B VAL* 4.5 5.2 - - + -
145B SER 4.2 0.2 - - - -
146B VAL* 1.3 76.3 - - - +
148B ARG* 1.3 68.2 + - - +
149B LEU* 4.1 22.4 + - + -
162B GLU 3.7 0.2 - - - +
163B SER* 3.4 1.6 - - - -
164B PHE* 2.8 44.6 + - + +
166B THR* 3.8 26.2 - - + -
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Residues in contact with ARG 148 (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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59B GLU* 2.4 34.5 + - - -
60B CYS* 3.6 27.8 - - + +
63B TYR* 4.2 7.2 - - - -
146B VAL* 5.1 3.1 - - + -
147B VAL* 1.3 81.1 - - - +
149B LEU* 1.3 68.9 + - - +
161B CYS* 3.4 39.1 + - - +
162B GLU* 3.0 8.9 + - - +
163B SER* 3.0 27.3 + - - +
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Residues in contact with LEU 149 (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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9B LEU* 4.2 22.0 - - + -
60B CYS* 3.7 5.4 - - - +
63B TYR* 3.9 18.6 - - + -
97B PRO* 4.6 3.8 - - + -
110B ILE* 4.0 29.6 - - + -
120B GLN* 3.6 23.3 - - + +
122B VAL* 3.9 22.4 - - + -
147B VAL* 4.1 9.8 + - + -
148B ARG* 1.3 83.3 - - - +
150B VAL* 1.3 65.6 + - - +
151B THR* 3.4 3.6 + - - +
161B CYS* 3.5 2.3 - - - -
162B GLU 3.0 28.1 + - - -
164B PHE* 4.1 17.0 - - + -
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Residues in contact with VAL 150 (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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56B VAL* 4.3 8.3 - - + -
57B PHE* 4.0 22.2 - - + -
60B CYS* 3.7 29.4 + - - +
61B GLY* 3.9 6.7 - - - +
110B ILE* 3.8 2.6 - - - +
111B VAL* 3.2 26.4 + - + -
118B PHE* 3.9 21.1 - - + -
120B GLN* 2.9 32.9 + - - +
149B LEU* 1.3 71.7 - - - +
151B THR* 1.3 63.9 + - - +
159B PHE* 3.9 22.7 - - + -
160B LEU 3.9 1.1 - - - -
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Residues in contact with THR 151 (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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108B ARG* 4.3 11.3 - - + -
109B VAL 3.3 15.3 - - - +
110B ILE* 4.5 2.5 - - + -
111B VAL* 3.6 4.3 - - - -
149B LEU 3.7 5.2 - - - +
150B VAL* 1.3 79.2 - - - +
152B TYR* 1.3 64.1 + - - +
153B ASN* 5.6 0.2 - - - -
159B PHE* 3.3 10.6 - - - -
160B LEU* 2.5 51.8 + - - +
162B GLU* 3.2 38.6 + - + +
164B PHE* 3.7 19.7 - - + -
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Residues in contact with TYR 152 (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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26B ILE* 5.2 2.7 - - + -
29B LYS* 3.4 29.6 + - + +
30B ILE* 3.8 39.0 - - + -
33B ALA* 4.1 21.1 - - + +
108B ARG* 5.6 2.9 - - - -
109B VAL* 3.1 21.1 + - + +
111B VAL* 3.8 6.2 - - + +
151B THR* 1.3 78.4 - - - +
153B ASN* 1.3 72.1 + - - +
154B LEU* 3.4 25.8 + - + +
157B ASP* 2.8 36.0 + - + +
158B GLY* 3.4 24.2 - - - -
159B PHE* 4.0 14.1 - + - -
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Residues in contact with ASN 153 (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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108B ARG* 5.9 4.6 + - - +
151B THR* 4.0 2.8 + - - +
152B TYR* 1.3 72.0 - - - +
154B LEU* 1.3 62.6 + - - +
155B GLU* 3.4 15.8 + - - +
156B LYS* 2.8 44.0 - - + +
157B ASP* 2.9 29.6 + - - -
158B GLY 2.8 16.9 + - - +
159B PHE* 4.9 0.2 - - - +
160B LEU* 4.4 26.7 - - + +
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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