Contacts of the strand formed by residues 158 - 172 (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 GLY 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B TYR* 3.4 12.9 - - - -
153B ASN* 2.8 31.0 + - - +
156B LYS* 3.1 7.9 + - - -
157B ASP* 1.3 75.8 - - - +
159B PHE* 1.3 67.9 + - - -
160B LEU* 5.6 0.2 - - - -
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Residues in contact with PHE 159 (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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30B ILE* 4.8 1.8 - - + -
33B ALA* 3.6 29.2 - - + -
34B VAL* 3.7 27.8 - - + -
37B VAL* 3.8 22.4 - - + -
54B HIS* 4.2 12.3 - - + -
56B VAL* 3.3 33.5 - - + +
57B PHE* 3.8 16.4 - + + -
111B VAL* 3.8 22.4 - - + -
150B VAL* 3.9 7.6 - - + -
151B THR 3.3 12.1 - - - +
152B TYR* 4.0 13.9 - + - -
158B GLY* 1.3 76.3 - - - -
160B LEU* 1.3 72.5 + - - +
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Residues in contact with LEU 160 (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* 3.9 9.2 - - + -
108B ARG* 5.7 1.8 - - - +
151B THR* 2.5 54.9 + - - +
153B ASN* 4.4 26.2 - - + +
158B GLY 4.1 0.4 + - - -
159B PHE* 1.3 82.1 - - - +
161B CYS* 1.3 62.5 + - - +
162B GLU* 3.9 16.2 - - - +
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Residues in contact with CYS 161 (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* 3.4 24.0 - - - +
59B GLU* 3.8 17.3 - - - +
60B CYS* 2.0 51.8 - - + -
148B ARG* 3.4 31.2 + - - +
149B LEU 3.5 0.7 - - - -
160B LEU* 1.3 77.3 - - - +
162B GLU* 1.3 70.8 + - - +
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Residues in contact with GLU 162 (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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102B THR* 3.5 18.4 - - + +
106B GLU* 4.8 1.0 - - - +
108B ARG* 2.9 37.8 + - + +
148B ARG* 3.0 11.2 + - - +
149B LEU 3.0 28.8 + - - -
151B THR* 3.2 35.6 + - + +
160B LEU* 3.9 18.6 - - - +
161B CYS* 1.3 79.9 - - - +
163B SER* 1.3 63.0 + - - +
164B PHE* 3.6 10.8 - - + -
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Residues in contact with SER 163 (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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102B THR* 3.2 8.9 - - - +
103B VAL* 2.8 41.6 + - - -
146B VAL* 3.7 19.7 - - - +
147B VAL 3.4 4.7 - - - -
148B ARG* 3.0 28.7 + - - +
162B GLU* 1.3 75.8 + - - +
164B PHE* 1.3 56.5 + - - +
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Residues in contact with PHE 164 (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* 3.9 22.0 - - + -
100B GLY* 3.5 31.9 - - - -
101B TYR 3.2 29.6 - - - +
102B THR* 3.7 5.2 - - + -
103B VAL* 4.2 4.3 - - - -
108B ARG* 3.9 11.7 - - + -
110B ILE* 3.9 15.3 - - + -
146B VAL* 3.3 2.4 - - - -
147B VAL* 2.8 44.0 + - + +
149B LEU* 4.1 17.5 - - + -
151B THR* 3.7 24.5 - - + -
162B GLU* 3.6 31.6 - - + -
163B SER* 1.3 73.6 - - - +
165B ARG* 1.3 64.0 + - - +
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Residues in contact with ARG 165 (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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8B CYS* 5.1 0.6 - - - -
9B LEU* 3.7 23.7 + - - +
101B TYR 4.8 5.1 + - - +
102B THR 5.8 0.7 - - - +
103B VAL* 3.1 57.2 + - + +
144B ARG* 3.5 55.7 + - + +
145B SER 3.0 9.4 - - - +
146B VAL* 4.5 7.7 - - + +
164B PHE* 1.3 75.2 - - - +
166B THR* 1.3 58.8 + - - +
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Residues in contact with THR 166 (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* 4.3 2.0 - - - -
73B SER* 4.8 2.6 - - - +
78B PHE* 3.9 19.3 - - + -
122B VAL* 3.2 12.8 - - + +
123B TRP 4.4 1.6 + - - -
124B GLN* 2.9 27.4 + - - +
144B ARG* 3.1 3.9 - - - -
145B SER* 2.7 51.1 + - - +
147B VAL* 3.8 32.5 - - + -
165B ARG* 1.3 74.6 - - - +
167B CYS* 1.3 66.4 + - - +
168B CYS* 3.4 0.9 + - + -
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Residues in contact with CYS 167 (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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7B ILE 4.0 2.5 - - - -
8B CYS* 2.0 53.8 - - - -
73B SER 4.3 0.3 - - - +
123B TRP 4.0 2.3 - - - +
124B GLN* 2.9 19.4 - - - +
125B HIS* 2.8 38.2 + - - +
126B LYS* 4.2 1.3 - - + -
142B GLN* 3.4 28.9 - - - +
143B GLN 3.7 4.5 - - - -
144B ARG* 3.9 12.3 - - - -
166B THR* 1.3 70.1 + - - +
168B CYS* 1.3 58.3 + - - +
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Residues in contact with CYS 168 (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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73B SER 3.1 23.3 - - - +
74B ARG* 2.8 22.4 + - - -
75B CYS* 2.0 59.3 + - - +
78B PHE* 4.5 1.3 - - + -
125B HIS* 3.6 8.2 - - - +
143B GLN* 3.0 25.3 + - - -
144B ARG 4.0 0.2 - - - -
145B SER* 3.9 23.1 - - - -
166B THR 3.4 4.2 + - - +
167B CYS* 1.3 73.4 - - - +
169B GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 169 (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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74B ARG* 3.5 2.7 - - - -
75B CYS* 3.3 11.6 - - - -
84B PHE* 4.4 0.4 - - - -
87B GLU* 3.2 12.6 - - - -
90B VAL* 4.6 0.7 - - - -
125B HIS* 3.5 9.8 + - - -
142B GLN* 2.6 27.7 + - - -
143B GLN* 2.7 15.9 + - - -
168B CYS* 1.3 80.4 - - - +
170B CYS* 1.3 56.9 + - - -
171B PRO* 3.8 5.6 - - - -
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Residues in contact with CYS 170 (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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87B GLU* 2.9 12.3 + - - +
88B CYS* 2.8 43.3 + - - +
89B PRO 4.3 2.0 - - - +
90B VAL* 4.0 12.3 - - + -
127B CYS* 2.0 59.9 - - - +
129B PHE 5.0 0.2 - - - -
140B CYS* 3.8 8.7 - - - -
141B THR 3.1 4.0 - - - -
169B GLY* 1.3 72.6 - - - -
171B PRO* 1.3 65.8 - - - +
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Residues in contact with PRO 171 (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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84B PHE* 3.6 25.4 - - + -
86B SER 3.9 6.1 - - - +
87B GLU* 3.9 4.5 - - + -
88B CYS* 4.5 0.2 - - - -
140B CYS* 3.8 0.7 - - - -
141B THR* 3.0 38.9 + - - +
143B GLN* 3.5 21.8 - - + +
170B CYS* 1.3 88.7 - - - +
172B CYS* 1.3 59.8 + - - +
173B ARG* 3.1 50.4 + - + +
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Residues in contact with CYS 172 (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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86B SER* 2.8 37.3 + - - +
87B GLU* 4.1 0.4 - - - +
88B CYS* 4.0 6.3 - - - +
134B CYS* 2.0 50.9 - - + -
135B GLY* 3.0 21.8 - - - -
138B GLY* 3.9 0.2 - - - -
170B CYS 3.7 1.6 + - - -
171B PRO* 1.3 70.3 - - - +
173B ARG* 1.3 63.5 + - - +
174B SER* 3.1 24.4 + - - -
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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