Contacts of the strand formed by residues 142 - 149 (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 ARG 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LYS* 3.8 19.2 - - + +
138B TRP* 3.5 3.2 - - - -
139B ASN 2.9 21.2 + - - +
140B GLU* 4.0 4.5 - - + +
141B GLY* 1.3 80.1 - - - +
143B PRO* 1.3 79.5 + - + +
144B TYR* 3.0 68.1 - - + +
145B LEU 4.6 1.4 - - - +
146B PHE* 5.2 0.2 - - - -
156B ALA* 4.4 16.2 - - - +
157B TRP 4.6 4.4 + - - -
57C ASP* 3.1 41.6 + - - +
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Residues in contact with PRO 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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38B LYS* 3.0 44.8 - - + +
40B ALA* 4.7 14.6 - - - +
42B GLY* 4.4 9.4 - - - +
43B VAL* 4.0 16.8 - - + +
137B GLY 3.4 1.8 - - - +
138B TRP* 2.3 42.8 - - + +
141B GLY 4.1 2.5 - - - +
142B ARG* 1.3 99.1 + - + +
144B TYR* 1.3 60.0 + - - +
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Residues in contact with TYR 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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43B VAL* 4.1 3.8 - - - +
106B THR* 3.1 23.3 - - + -
107B ALA* 5.2 6.7 - - + -
136B CYS* 3.2 4.3 - - - +
137B GLY 2.0 70.7 + - - +
139B ASN* 3.3 20.3 - - + +
140B GLU* 1.9 37.2 + - - -
142B ARG* 3.0 60.0 - - + +
143B PRO* 1.3 68.5 - - - +
145B LEU* 1.3 59.9 + - - +
146B PHE* 3.7 28.7 - + + -
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Residues in contact with LEU 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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36B GLY 3.5 27.4 - - - +
38B LYS* 3.9 7.6 - - + +
43B VAL* 4.0 18.4 - - + -
45B LEU* 3.7 29.8 - - + -
134B LEU* 4.7 1.1 - - + -
135B ILE 4.1 1.1 - - - -
136B CYS* 4.1 2.7 - - + +
142B ARG* 4.6 2.0 - - - +
143B PRO 4.2 0.6 + - - -
144B TYR* 1.3 76.0 - - - +
146B PHE* 1.4 62.4 + - - +
156B ALA* 3.3 5.7 - - - +
157B TRP* 2.8 43.7 + - + +
158B LYS 3.8 4.9 - - - -
159B ALA* 3.7 25.8 - - - +
160B THR* 3.8 19.5 - - + -
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Residues in contact with PHE 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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106B THR* 4.0 3.1 - - + -
107B ALA* 3.6 38.6 - - + -
110B VAL* 3.7 27.8 - - + -
134B LEU* 3.2 13.1 - - - +
135B ILE* 2.9 39.4 + - + +
142B ARG* 5.2 0.2 - - - -
144B TYR* 3.7 33.2 - + + -
145B LEU* 1.4 77.6 - - - +
147B GLN* 1.3 58.2 + - - +
154B TYR* 3.7 31.9 - + - -
155B PHE 3.4 3.1 - - - -
156B ALA* 3.6 33.0 - - + -
157B TRP* 5.3 1.8 - - - -
160B THR* 5.6 0.2 - - - -
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Residues in contact with GLN 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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132B SER* 3.1 2.0 + - - -
133B LEU 3.4 4.6 + - - -
134B LEU* 3.5 6.1 - - + +
146B PHE* 1.3 75.7 - - - +
148B SER* 1.4 69.6 + - - +
149B ASP* 3.0 35.2 + - - +
153B ALA 4.0 0.3 - - - +
154B TYR* 3.1 5.8 - - - -
155B PHE* 2.8 40.9 + - + +
157B TRP* 4.2 17.0 - - + +
160B THR* 4.0 7.0 + - - +
161B ALA 4.1 1.7 - - - +
162B MET* 2.6 51.0 - - - +
170B LYS* 4.8 6.5 + - - +
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Residues in contact with SER 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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110B VAL* 4.7 2.8 + - - +
113B VAL* 5.0 2.2 - - - -
114B ALA* 4.1 16.3 + - - +
117B MET* 3.6 22.9 - - - -
132B SER* 2.9 8.4 + - - -
133B LEU* 2.9 32.2 + - - -
135B ILE* 4.3 18.8 - - - +
146B PHE 4.2 0.6 - - - -
147B GLN* 1.4 70.7 + - - +
149B ASP* 1.4 69.7 + - - +
152B GLY* 4.7 0.5 - - - -
153B ALA 3.7 6.9 + - - -
154B TYR* 3.9 11.7 - - - +
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Residues in contact with ASP 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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25B LEU* 5.0 7.1 - - + +
28B VAL* 5.9 1.6 - - - -
117B MET* 3.2 17.2 - - - +
131B VAL 4.4 0.2 - - - -
132B SER* 2.1 30.3 + - - -
147B GLN* 3.0 24.9 + - - +
148B SER* 1.4 76.1 - - - +
150B PRO* 1.3 68.9 - - + +
151B SER* 3.3 5.4 - - - +
152B GLY* 3.0 18.2 + - - -
153B ALA* 3.0 17.6 + - + +
155B PHE* 4.4 12.1 - - - -
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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