Contacts of the strand formed by residues 25 - 31 (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 SER 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER 3.8 1.5 + - - -
24A SER* 1.3 77.4 - - - +
26A TYR* 1.3 64.2 + - - +
133A LEU* 3.2 51.6 + - - -
134A HIS* 4.4 3.5 + - - -
137A THR* 5.1 0.2 + - - -
156A HIS* 3.7 4.3 + - - +
157A TRP* 2.9 45.8 + - - +
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Residues in contact with TYR 26 (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* 1.3 78.7 - - - +
27A SER* 1.3 74.7 + - - +
28A GLY* 3.6 21.4 + - - -
29A GLU* 3.3 35.3 + - - +
143A SER* 4.0 3.6 + - - -
154A GLY* 3.7 11.7 - - - -
155A LEU 3.4 11.9 - - - -
156A HIS* 3.3 41.3 - + + +
157A TRP* 4.5 1.1 - - - -
204A CL 4.6 12.3 - - + -
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 1.3 77.0 + - - +
28A GLY* 1.3 58.3 + - - +
30A TYR* 3.6 10.5 - - - -
130A ALA* 3.5 28.8 - - - +
131A VAL 3.7 12.6 + - - -
154A GLY* 3.3 4.3 - - - -
155A LEU* 2.8 41.1 + - - -
157A TRP* 2.9 26.0 + - - +
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Residues in contact with GLY 28 (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* 3.6 16.1 - - - -
27A SER* 1.3 74.5 - - - +
29A GLU* 1.3 65.8 + - - -
30A TYR* 3.5 22.9 + - - -
153A ILE 4.3 0.4 - - - -
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Residues in contact with GLU 29 (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* 3.3 19.1 + - - +
28A GLY* 1.3 71.3 + - - -
30A TYR* 1.3 65.3 + - - +
31A GLY 3.9 3.7 + - - +
32A SER 4.7 1.4 - - - +
101A TYR* 5.6 0.3 + - - -
143A SER* 4.9 1.7 + - - -
144A GLY* 3.4 26.2 + - - +
145A ARG* 3.7 22.8 + - - +
152A ALA* 3.7 22.9 - - + +
153A ILE 3.7 8.5 - - - +
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Residues in contact with TYR 30 (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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27A SER* 3.6 21.4 - - - -
28A GLY* 3.5 24.5 + - - -
29A GLU* 1.3 73.5 - - - +
31A GLY* 1.3 58.0 + - - +
101A TYR* 4.0 15.0 - + + -
105A LEU* 4.5 4.2 - - - +
128A PHE* 3.5 68.9 - + + -
129A ASN 4.4 3.9 + - - -
130A ALA* 3.7 10.9 - - + +
152A ALA* 3.1 3.3 - - - -
153A ILE* 2.8 53.9 + - + +
155A LEU* 3.7 13.9 - - + -
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Residues in contact with GLY 31 (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 3.9 4.1 + - - +
30A TYR* 1.3 73.7 - - - +
32A SER* 1.3 64.6 + - - -
101A TYR* 3.6 39.3 - - - -
102A LYS 4.5 1.5 - - - +
103A TRP 5.1 0.4 - - - -
105A LEU 5.5 0.2 - - - -
151A ASP 3.4 9.6 - - - -
152A ALA* 3.9 2.0 - - - -
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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