Contacts of the strand formed by residues 150 - 158 (chain A) in PDB entry 3VY7
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 ILE 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A PHE* 4.6 2.5 - - + -
61A ILE* 3.0 27.4 + - + +
62A VAL 4.0 3.6 - - - +
63A GLY* 4.0 5.4 - - - -
64A LEU* 3.8 28.9 - - + +
76A VAL* 3.9 24.5 - - + +
77A GLY* 4.0 0.7 - - - -
104A TYR* 3.6 5.9 - - - +
105A LEU* 2.9 50.7 + - + +
145A ARG 3.7 2.9 - - - +
146A SER* 3.7 22.2 - - - -
149A LEU* 1.3 74.6 - - - +
151A ASP* 1.3 58.3 + - - +
152A ALA 3.4 24.5 - - - +
153A ILE* 4.8 0.2 - - + -
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Residues in contact with ASP 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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31A GLY* 3.4 5.2 - - - -
32A SER 2.9 23.5 + - - +
34A GLY* 3.3 35.0 - - - +
35A GLY* 3.6 1.9 - - - -
103A TRP 3.5 13.1 - - - +
104A TYR* 3.4 17.9 - - - +
105A LEU 4.1 1.6 + - - -
145A ARG* 2.9 11.9 + - + +
146A SER 3.4 5.4 - - - -
147A GLY 3.3 13.3 + - - -
150A ILE* 1.3 74.2 - - - +
152A ALA* 1.3 58.9 + - - +
202A MAN 2.6 45.9 + - - -
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Residues in contact with ALA 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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29A GLU* 3.7 24.9 - - + +
30A TYR 3.1 13.7 - - - +
31A GLY* 3.9 1.6 - - - -
32A SER 3.5 20.6 - - - +
38A PHE* 4.2 1.0 - - - -
105A LEU* 5.3 2.2 - - - -
144A GLY* 3.2 2.4 - - - -
145A ARG* 2.9 30.7 + - + +
150A ILE* 3.4 13.3 - - - +
151A ASP* 1.3 81.4 - - - +
153A ILE* 1.3 61.1 + - - +
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Residues in contact with ILE 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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29A GLU* 4.1 5.4 - - - -
30A TYR* 2.8 39.6 + - + +
38A PHE* 5.2 0.4 - - + -
64A LEU* 4.0 24.5 - - + -
105A LEU* 3.7 29.6 - - + -
108A LEU* 4.0 23.1 - - + -
110A PHE* 5.2 3.4 - - + -
128A PHE* 4.2 18.6 - - + -
142A ILE* 4.2 15.0 - - + -
143A SER 3.4 13.5 - - - +
150A ILE* 4.8 0.7 - - + -
152A ALA* 1.3 75.5 - - - +
154A GLY* 1.3 67.5 + - - +
155A LEU* 4.4 14.4 - - + -
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Residues in contact with GLY 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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26A TYR* 3.7 22.9 - - - -
27A SER 3.3 11.4 - - - -
29A GLU* 4.6 0.2 - - - +
142A ILE* 3.4 8.5 - - - +
143A SER* 2.8 34.8 + - - +
144A GLY* 4.3 0.4 - - - -
153A ILE* 1.3 74.6 - - - +
155A LEU* 1.3 66.4 + - - +
156A HIS* 4.2 0.2 - - - -
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Residues in contact with LEU 155 (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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26A TYR* 3.4 5.7 - - - -
27A SER* 2.8 35.5 + - - +
30A TYR* 3.7 31.4 - - + -
97A VAL* 3.9 39.5 - - + -
110A PHE* 5.0 1.8 - - + -
128A PHE* 4.2 7.2 - - + -
130A ALA* 3.8 12.3 - - + -
139A LEU* 3.7 18.8 - - + -
141A PHE 4.2 0.4 - - - -
142A ILE* 4.1 12.3 - - + -
153A ILE* 4.4 13.0 - - + -
154A GLY* 1.3 80.5 - - - +
156A HIS* 1.3 63.2 + - - +
157A TRP* 3.9 17.8 + - + +
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Residues in contact with HIS 156 (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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25A SER 3.7 4.9 + - - +
26A TYR* 3.3 28.7 - + + +
39A SER* 5.5 0.4 - - - -
139A LEU* 3.7 3.6 - - - +
140A ARG* 2.9 27.3 + - - +
141A PHE* 3.0 69.2 + + + +
143A SER* 2.8 37.0 + - - -
154A GLY 3.9 0.4 - - - -
155A LEU* 1.3 78.7 - - - +
157A TRP* 1.3 63.4 + - - +
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Residues in contact with TRP 157 (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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24A SER* 3.3 4.6 - - - -
25A SER* 2.9 58.0 + - - +
27A SER* 2.9 27.7 + - - -
94A VAL 3.6 20.4 - - - -
95A ILE 3.7 11.9 - - - -
96A GLN* 3.8 23.3 - - - -
97A VAL* 3.9 12.8 - - + -
130A ALA* 3.7 23.1 - - + -
131A VAL 3.9 1.8 + - - -
132A PRO* 3.6 32.5 - - + -
137A THR* 4.2 4.9 - - - +
138A VAL* 3.2 10.1 - - - +
139A LEU* 3.4 28.3 - - + -
155A LEU* 3.9 23.5 + - + -
156A HIS* 1.3 74.7 - - - +
158A ASP* 1.3 65.7 + - - +
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Residues in contact with ASP 158 (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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23A SER* 4.0 5.2 - - - -
24A SER* 3.7 27.3 + - - +
44A GLN* 5.1 6.0 - - - +
137A THR* 3.5 12.7 - - - -
138A VAL* 3.0 31.2 + - - +
140A ARG* 3.6 20.3 - - + +
141A PHE* 6.4 0.7 - - + -
157A TRP* 1.3 77.3 - - - +
159A VAL* 1.3 92.3 + - - +
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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