Contacts of the strand formed by residues 132 - 139 (chain B) 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 SER 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.6 34.4 - - - +
75B TYR* 3.5 1.4 - - - +
76B SER* 2.9 32.3 + - - +
117B MET* 5.2 0.2 - - - -
130B GLY 3.6 0.8 + - - -
131B VAL* 1.3 72.7 - - - +
133B LEU* 1.3 62.4 + - - +
147B GLN* 3.1 6.1 + - - -
148B SER 2.9 8.2 + - - -
149B ASP* 2.1 34.7 + - - +
150B PRO* 4.0 4.3 - - - -
162B MET* 3.6 4.6 - - - +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 2.8 27.6 - - + -
74B VAL 3.1 16.8 - - - +
75B TYR* 3.9 7.4 - - + -
82B TYR* 4.4 4.3 - - + -
85B LEU* 3.2 36.8 - - + -
113B VAL* 5.5 0.7 - - + -
117B MET* 5.9 2.9 - - + -
131B VAL* 3.9 13.9 - - + -
132B SER* 1.3 76.0 + - - +
134B LEU* 1.3 59.0 + - - +
135B ILE* 2.7 46.9 - - + -
147B GLN* 3.5 5.2 - - - -
148B SER* 2.9 38.1 + - - -
162B MET* 3.6 1.6 - - - -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B SER* 4.6 2.0 - - - -
35B VAL* 3.6 39.9 - - - +
36B GLY* 3.7 6.3 - - - +
45B LEU* 3.9 24.2 - - + -
73B LEU* 3.3 5.0 - - - -
74B VAL* 2.9 34.2 + - + +
133B LEU* 1.3 72.2 - - - +
135B ILE* 1.3 60.9 + - - +
136B CYS 3.9 0.4 - - - -
145B LEU* 4.7 1.1 - - + -
146B PHE 3.2 9.4 - - - +
147B GLN* 3.5 10.8 - - - +
160B THR* 3.4 27.4 - - + -
162B MET* 2.9 42.5 - - + +
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Residues in contact with ILE 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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67B ILE* 6.5 0.2 - - + -
71B ILE* 3.5 20.4 - - + -
72B GLY 3.4 15.0 - - - +
73B LEU* 3.5 9.0 - - + -
106B THR* 4.7 0.6 - - + +
109B LEU* 5.6 4.9 - - + -
110B VAL* 3.8 41.9 - - + +
113B VAL* 4.7 15.0 - - + -
133B LEU* 2.7 40.6 - - + +
134B LEU* 1.3 72.5 - - - +
136B CYS* 1.3 58.6 + - - +
137B GLY 3.9 0.2 + - - -
146B PHE* 2.9 35.8 + - + +
148B SER* 4.3 11.9 - - - +
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Residues in contact with CYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.4 34.5 - - + -
45B LEU* 3.5 36.0 - - + +
71B ILE* 3.7 4.1 - - - -
72B GLY 3.3 25.7 + - - -
106B THR* 4.4 0.9 - - - -
134B LEU 3.9 1.0 - - - -
135B ILE* 1.3 72.7 - - - +
137B GLY* 1.3 57.5 + - - +
144B TYR 3.2 6.1 - - - +
145B LEU* 4.1 4.3 - - + +
210B GLY 5.6 0.7 - - - -
212B CYS* 3.8 11.0 - - - -
217B PHE* 3.7 21.1 - - - -
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Residues in contact with GLY 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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43B VAL* 5.5 1.5 - - - +
70B HIS 3.8 9.9 - - - -
71B ILE* 4.4 2.0 - - - -
106B THR* 3.3 21.5 - - - +
136B CYS* 1.3 68.9 - - - +
138B TRP* 1.3 54.5 + - - -
143B PRO* 3.1 0.7 - - - +
144B TYR* 2.0 68.4 + - - +
212B CYS* 4.4 3.4 - - - -
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Residues in contact with TRP 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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40B ALA 5.5 1.2 + - - -
41B ASN 4.2 7.8 + - - -
42B GLY* 4.4 7.4 - - - -
43B VAL 5.1 0.2 - - - -
70B HIS* 3.4 30.6 + - + +
71B ILE* 5.5 0.2 - - - +
106B THR* 3.9 1.6 + - - -
137B GLY* 1.3 73.2 - - - -
139B ASN* 1.3 69.1 + - - +
140B GLU* 3.2 27.8 - - - -
141B GLY* 3.3 32.5 - - - -
142B ARG 3.4 5.2 - - - -
143B PRO* 2.3 47.6 - - + +
212B CYS* 4.5 5.8 - - + -
213B ASN 3.5 28.4 + - - +
214B GLU* 5.1 20.4 - - + -
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Residues in contact with ASN 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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70B HIS* 5.8 3.0 - - - +
71B ILE* 6.0 1.0 - - - +
103B PRO* 4.3 21.2 + - - +
104B ILE 4.5 3.4 + - - -
105B PRO* 3.5 8.0 - - + +
106B THR* 2.7 40.1 + - - -
138B TRP* 1.3 83.2 + - - +
140B GLU* 1.3 69.3 + - + +
141B GLY 3.0 0.5 + - - -
142B ARG 2.9 31.5 + - - +
144B TYR* 3.3 12.6 - - + +
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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
------------------------------------------------------------
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