Contacts of the strand formed by residues 147 - 154 (chain A) in PDB entry 3N56
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 THR 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 3.7 2.4 - - - +
91A ASP* 3.5 2.2 - - - -
92A VAL* 2.8 38.4 + - - +
94A ILE* 2.8 17.8 + - - +
95A GLY* 4.1 1.2 - - - -
107A SER* 4.8 4.8 - - - +
111A GLN* 3.7 17.5 - - + -
141A PHE 3.6 3.8 - - - +
142A THR* 3.8 19.7 - - + +
146A HIS* 1.3 74.1 + - - +
148A ASN* 1.3 61.5 + - - +
149A TYR* 3.4 21.5 - - + +
249A TYR* 3.3 28.6 + - - +
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Residues in contact with ASN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 3.5 4.3 - - - -
91A ASP* 2.7 32.2 + - - +
140A ALA* 3.2 21.7 - - - +
141A PHE* 3.1 43.8 + - + +
146A HIS* 5.4 0.4 - - + -
147A THR* 1.3 73.4 - - - +
149A TYR* 1.3 62.6 + - - +
150A TYR* 3.2 10.6 - - - -
435A SER* 2.7 48.0 + - - -
438A ALA* 4.3 2.0 - - - +
439A GLY* 4.1 2.8 - - - +
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Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA* 3.1 6.1 - - - +
90A LEU 2.9 38.3 + - - +
92A VAL* 4.7 1.3 - - + -
110A LEU* 3.9 0.5 - - - +
111A GLN* 3.3 37.5 - - + +
114A LEU* 3.3 27.3 - - + +
115A PHE* 4.1 12.1 - + + -
139A ASN 4.0 3.8 - - - -
140A ALA* 4.0 11.0 - - + -
147A THR* 3.4 31.0 - - + -
148A ASN* 1.3 76.7 + - - +
150A TYR* 1.3 63.0 + - - +
165A PHE* 3.6 20.6 - - + -
168A PHE* 4.3 9.9 - + - -
169A PHE* 3.9 13.7 - + + -
249A TYR* 2.6 32.2 + + - -
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA 3.4 6.3 - - - +
89A ALA* 3.7 15.9 - - + -
138A SER* 2.6 23.1 + - - -
139A ASN* 3.0 64.3 + - + +
140A ALA* 4.0 10.6 + - - -
141A PHE* 4.1 14.8 - + - +
148A ASN* 3.2 21.8 - - - -
149A TYR* 1.3 76.7 - - - +
151A PHE* 1.3 59.4 + - - +
165A PHE* 4.0 4.9 - - - -
431A ARG* 3.5 40.9 + - + +
432A GLY* 6.3 0.4 - - - -
434A THR* 4.8 0.2 - - - +
435A SER* 3.3 19.3 - - - -
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A SER* 2.8 33.5 + - - -
88A ALA* 3.1 45.5 + - + -
127A TYR* 3.4 25.1 - - - +
131A LEU* 4.0 12.1 - - + -
137A SER 3.2 13.5 - - - +
138A SER* 3.6 3.6 - - - +
150A TYR* 1.3 74.4 - - - +
152A ASP* 1.3 69.8 + - - +
153A VAL* 3.9 11.7 - - + -
158A LEU* 4.4 6.7 - - + -
161A ALA* 3.7 15.7 - - + -
162A LEU* 3.9 23.8 - - + -
165A PHE* 3.6 30.3 - + + -
431A ARG* 4.2 8.2 - - - +
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Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS* 4.2 31.5 + - + +
86A SER 3.2 13.2 - - - +
87A SER* 4.1 7.2 - - - -
131A LEU* 3.5 7.1 - - - +
136A GLY* 2.8 28.1 - - - -
137A SER* 3.0 32.7 + - - -
151A PHE* 1.3 76.9 - - - +
153A VAL* 1.3 60.0 + - - +
430A PRO* 5.4 1.6 - - + +
431A ARG* 3.2 35.7 + - + +
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS* 3.3 10.4 - - - +
86A SER 2.8 29.0 + - - +
130A PHE* 4.7 2.0 - - + -
131A LEU* 4.0 18.2 - - + +
134A HIS* 3.4 29.6 - - + +
135A ALA 4.5 0.4 - - - -
136A GLY* 3.7 8.7 - - - +
151A PHE* 3.9 9.0 - - + -
152A ASP* 1.3 77.9 + - - +
154A SER* 1.3 82.9 + - - +
157A HIS* 3.8 27.4 - - + +
158A LEU* 4.1 5.6 - - - -
161A ALA* 3.8 13.5 - - + -
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP 4.2 7.4 - - - -
85A LYS* 4.7 2.2 - - - +
86A SER* 4.3 0.5 - - - -
134A HIS* 2.6 26.6 + - - -
135A ALA* 4.1 3.0 + - - +
153A VAL* 1.3 86.9 - - - +
155A HIS* 1.3 62.1 + - - +
156A GLU* 2.9 14.4 + - - -
157A HIS* 3.2 31.8 + - - -
158A LEU 3.8 1.2 + - - -
891A ILE* 3.3 33.0 - - - +
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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