Contacts of the strand formed by residues 148 - 155 (chain O) in PDB entry 5A0Q
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 148 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143O ILE* 4.0 9.9 - - - -
144O ASP* 2.9 34.6 + - - +
149O PRO* 1.3 78.7 - - - +
150O GLN* 3.6 10.8 + - - +
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Residues in contact with PRO 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O ARG* 2.7 36.0 - - + -
44O GLY 3.4 15.3 - - - +
45O LYS* 3.3 28.7 - - - +
46O ASP* 4.7 1.1 - - - -
47O CYS* 4.1 8.1 - - - +
48O ALA* 3.9 21.3 - - + -
142O GLY 3.9 6.7 - - - +
143O ILE* 4.0 18.8 - - + -
148O GLY* 1.3 84.6 - - - +
150O GLN* 1.3 65.9 + - - +
222O VAL* 6.2 1.3 - - + -
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Residues in contact with GLN 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O ARG* 3.7 10.3 - - - +
48O ALA* 4.5 1.7 - - - +
111O VAL* 3.8 26.0 - - + -
112O ASP* 4.5 8.5 - - - +
140O LEU 4.3 0.4 - - - -
141O ILE* 3.5 22.4 - - - +
142O GLY 3.0 17.0 + - - +
144O ASP* 4.1 17.1 - - + +
148O GLY 3.6 14.6 + - - +
149O PRO* 1.3 93.5 + - - +
151O VAL* 1.4 69.6 + - - +
152O TYR* 3.3 29.5 + - + -
57P ASP* 5.8 0.6 + - - -
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Residues in contact with VAL 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O ALA* 3.8 12.8 - - + +
42O VAL 4.2 5.4 - - - +
43O ARG* 3.4 41.7 - - + +
48O ALA* 5.0 1.8 - - + -
139O ILE* 4.1 4.0 - - + -
140O LEU 3.5 4.7 - - - +
141O ILE* 4.1 10.5 - - + -
150O GLN* 1.4 78.4 - - - +
152O TYR* 1.3 61.9 + - - +
163O PHE* 3.1 32.5 + - + +
164O LYS 4.7 0.9 - - - +
166O THR* 3.5 42.0 - - + +
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Residues in contact with TYR 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O ARG* 5.0 2.0 - - - -
111O VAL* 4.4 6.3 - - + -
112O ASP* 3.2 37.5 + - + +
115O CYS* 3.6 28.5 - - + -
138O MET 3.5 0.6 - - - +
139O ILE* 3.3 8.0 - - - +
140O LEU* 3.0 38.2 + - + +
150O GLN* 3.3 41.5 + - + -
151O VAL* 1.3 81.6 - - - +
153O LYS* 1.3 58.8 + - - +
160O TYR* 3.7 28.0 - + - -
161O CYS* 3.7 8.3 - - - -
162O GLY* 3.9 19.0 - - - -
166O THR* 5.6 0.4 - - - -
57P ASP* 5.7 1.6 + - - -
60P SER* 4.1 16.0 - - - -
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Residues in contact with LYS 153 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115O CYS* 3.4 3.9 - - - -
137O CYS* 3.6 24.9 - - - -
138O MET 3.6 4.7 - - - +
139O ILE* 4.8 3.4 - - + +
151O VAL 3.9 0.4 + - - -
152O TYR* 1.3 72.7 - - - +
154O CYS* 1.4 61.5 + - - +
155O ASP* 3.1 36.7 + - - +
159O TYR* 4.2 19.7 + - - -
160O TYR* 3.3 27.8 - - - +
161O CYS* 3.0 18.4 + - - +
163O PHE* 3.8 28.7 - - + -
166O THR* 3.9 23.8 - - - +
167O ALA 5.2 5.6 - - - +
168O ALA* 5.3 1.3 - - + -
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Residues in contact with CYS 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O GLN* 5.8 2.5 - - - -
115O CYS* 3.9 14.6 - - - -
118O ILE* 4.7 6.7 - - - -
119O ALA* 3.6 39.9 - - - -
122O SER* 4.3 3.4 - - - -
136O CYS 5.2 0.4 - - - -
137O CYS* 3.4 13.0 - - - -
138O MET* 3.1 45.2 + - + -
153O LYS* 1.4 75.7 - - - +
155O ASP* 1.3 76.0 + - - +
159O TYR 3.5 7.9 - - - -
160O TYR* 4.7 0.2 - - - -
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Residues in contact with ASP 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O PHE* 4.0 20.7 - - + -
32O ILE* 5.1 2.8 - - - +
122O SER* 3.5 4.2 + - - -
136O CYS 5.1 2.9 - - - -
137O CYS* 4.3 7.8 - - - -
153O LYS* 3.1 31.2 + - - +
154O CYS* 1.3 86.8 - - - +
156O PRO* 1.3 67.3 - - + +
157O ALA* 2.9 23.5 + - + +
158O GLY 3.3 9.0 + - - -
159O TYR* 3.2 20.1 + - + +
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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