Contacts of the strand formed by residues 143 - 150 (chain B) in PDB entry 5N4D
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 ALA 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLN* 3.1 15.9 + - - -
134B PRO 4.0 6.8 - - - +
135B ASN 5.5 0.5 - - - +
137B LEU* 3.8 19.0 - - + +
138B ALA* 3.8 17.7 + - + +
141B GLY* 3.2 7.2 - - - +
142B SER* 1.3 80.7 - - - +
144B GLY* 1.3 57.7 + - - +
161B VAL* 4.1 4.3 - - + -
162B SER 3.2 11.0 - - - +
163B HIS* 3.7 23.6 - - + +
700B MET* 4.1 4.0 - - - -
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Residues in contact with GLY 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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106B GLN* 3.3 15.0 - - - -
137B LEU* 3.9 6.1 - - - -
143B ALA* 1.3 75.3 - - - +
145B MET* 1.3 62.2 + - - -
146B VAL* 3.7 5.1 + - - +
161B VAL* 3.4 4.9 - - - +
162B SER 2.9 32.5 + - - -
700B MET* 3.8 15.0 - - - +
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Residues in contact with MET 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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98B PHE* 3.8 34.8 - - + -
106B GLN* 3.0 11.1 + - - +
132B PHE* 3.4 25.8 - - + -
134B PRO* 3.7 22.2 - - + -
137B LEU* 3.8 10.6 - - + +
144B GLY* 1.3 72.7 - - - -
146B VAL* 1.3 63.8 + - - +
147B LEU 3.7 11.4 - - - +
148B CYS* 3.8 26.2 - - - -
157B PHE* 4.0 1.8 - - - -
159B TYR* 4.0 10.5 - - + -
160B ALA 3.5 13.0 - - - +
161B VAL* 5.3 0.2 - - + -
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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
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144B GLY* 4.0 10.1 - - - +
145B MET* 1.3 80.0 - - - +
147B LEU* 1.3 69.2 + - + +
160B ALA* 3.0 21.1 + - + +
162B SER* 3.8 18.6 - - - +
169B SER* 3.9 11.4 - - - +
200B PHE* 5.7 1.3 - - + -
698B HIS 3.1 24.5 - - - +
699B GLY* 3.7 24.2 - - - +
700B MET* 4.2 3.1 - - + +
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Residues in contact with LEU 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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145B MET* 3.7 7.0 - - - +
146B VAL* 1.3 84.4 - - + +
148B CYS* 1.3 72.4 + - - +
159B TYR* 3.5 0.5 - - - -
160B ALA* 2.9 35.7 + - + -
200B PHE* 3.8 16.6 - - + -
203B SER 3.4 25.6 - - - +
204B THR* 3.9 19.1 - - + -
205B ILE* 4.2 10.3 - - + +
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Residues in contact with CYS 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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98B PHE* 4.0 15.0 - - - -
109B LEU* 4.9 0.2 - - - -
145B MET* 3.8 21.8 - - - -
147B LEU* 1.3 87.2 - - - +
149B LYS* 1.3 71.4 + - - +
157B PHE* 3.4 34.3 - - + -
158B ALA 3.2 14.1 - - - +
159B TYR* 4.1 0.9 - - + +
205B ILE* 4.8 4.0 - - - -
23D ASP 4.3 2.3 - - - +
24D ILE* 4.1 23.2 - - - +
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Residues in contact with LYS 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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148B CYS* 1.3 78.8 - - - +
150B PHE* 1.3 63.8 + - - +
157B PHE* 4.5 2.2 - - - -
158B ALA* 2.9 32.5 + - - +
204B THR* 5.1 3.8 - - - -
205B ILE* 2.8 45.2 + - + +
206B ILE* 3.8 17.6 - - - +
207B TRP* 3.0 29.7 + - + +
23D ASP* 3.5 43.0 + - - +
24D ILE 3.5 8.7 - - - -
25D CYS* 4.0 17.5 - - - +
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Residues in contact with PHE 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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90B LEU* 3.5 38.8 - - + -
96B TYR* 3.6 28.7 - + + -
109B LEU* 3.8 14.1 - - + -
131B PHE* 3.6 14.6 - + - -
149B LYS* 1.3 78.7 - - - +
151B SER* 1.3 69.7 + - - +
152B PRO* 3.7 1.0 - - - +
154B GLY* 5.2 0.4 - - - -
156B PHE 3.4 5.8 - - - -
157B PHE* 3.4 28.0 - + - +
176B THR* 3.5 29.8 - - + -
207B TRP* 3.4 11.4 - - - -
24D ILE* 2.7 41.1 + - + +
25D CYS* 3.7 11.9 - - - +
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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