Contacts of the strand formed by residues 56 - 61 (chain A) in PDB entry 4HVY
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 GLU 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE 3.5 0.9 - - - +
51A LEU* 3.3 4.4 - - - -
52A SER* 2.8 36.4 + - - +
54A GLN* 3.7 20.8 - - - +
55A ASP* 1.3 79.9 - - - +
57A VAL* 1.3 62.6 + - - +
144A TRP* 3.5 35.2 - - + +
145A TYR 3.2 12.3 - - - +
146A PRO* 4.0 23.4 - - + +
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Residues in contact with VAL 57 (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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49A VAL* 4.9 1.6 - - + -
50A PHE 3.2 10.8 - - - +
51A LEU* 3.9 5.4 - - + -
56A GLU* 1.3 76.0 - - - +
58A LEU* 1.3 64.4 + - - +
59A LEU* 3.6 13.0 + - + +
73A LEU* 3.7 28.3 - - + -
143A ALA 3.6 0.2 - - - +
144A TRP* 3.3 6.1 - - - -
145A TYR* 2.8 36.0 + - - +
147A ARG* 3.9 20.9 - - + -
150A LEU* 4.7 7.4 - - + -
163A VAL* 3.5 40.2 - - + -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.5 47.0 + - + -
57A VAL* 1.3 72.6 - - - +
59A LEU* 1.3 71.4 + - - +
73A LEU* 3.6 2.4 - - - +
74A PRO* 3.7 10.3 - - + +
92A VAL* 5.0 0.4 - - + -
96A ALA* 3.9 22.0 - - + -
98A LEU* 4.0 16.8 - - + -
129A LEU* 3.7 28.5 - - + -
142A ALA* 4.2 2.7 - - + -
143A ALA 3.7 16.2 - - - +
144A TRP* 3.6 21.8 - - + +
203A MG 2.7 21.4 - - - -
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Residues in contact with LEU 59 (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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57A VAL* 4.0 10.3 - - + +
58A LEU* 1.3 81.7 - - - +
60A ILE* 1.3 65.5 + - - +
71A TRP* 3.8 18.4 - - + -
72A TYR 3.3 21.3 - - - +
73A LEU* 3.6 20.2 - - + -
142A ALA* 3.3 5.0 - - - +
143A ALA 2.9 35.1 + - - +
145A TYR* 4.0 7.6 - - + -
150A LEU* 4.0 18.6 - - + -
151A PRO* 3.4 35.7 - - + -
154A LEU* 4.9 5.8 - - + -
159A ILE* 4.0 9.6 - - + -
163A VAL* 5.8 1.1 - - + -
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Residues in contact with ILE 60 (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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58A LEU* 5.2 0.4 - - + -
59A LEU* 1.3 79.2 - - - +
61A GLN* 1.3 67.5 + - - +
62A GLU* 3.7 33.0 - - - +
71A TRP* 3.3 7.7 - - - -
72A TYR 2.8 38.5 + - - +
73A LEU 4.0 6.7 - - - +
74A PRO* 3.9 22.9 - - + -
95A GLU* 3.6 54.1 - - + +
96A ALA* 4.0 3.1 - - + -
138A GLU 4.7 0.7 - - - +
139A SER* 4.1 9.6 - - - -
141A GLN 3.5 4.7 - - - +
142A ALA* 4.0 5.8 - - + -
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Residues in contact with GLN 61 (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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60A ILE* 1.3 73.9 - - - +
62A GLU* 1.3 62.3 + - - +
69A GLY* 3.0 33.6 + - - +
70A SER 3.4 11.4 - - - +
71A TRP* 3.6 33.7 - - + +
139A SER* 3.4 5.2 - - - -
140A LEU* 2.8 46.9 + - + +
141A GLN* 2.9 41.5 + - + +
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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