Contacts of the strand formed by residues 74 - 78 (chain A) in PDB entry 3U3S
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 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A CYS* 3.4 5.9 - - - +
71A PRO* 2.6 49.0 + - + +
72A ALA 5.0 0.9 - - - +
73A GLY* 1.3 84.3 - - - +
75A TYR* 1.3 61.4 + - - +
88A CYS* 3.8 11.3 - - + +
89A SER 2.9 22.4 - - - +
90A SER* 3.7 11.9 - - - -
91A CYS* 4.1 3.4 - - - -
97A THR* 3.2 8.8 + - - +
101A ASN* 3.0 22.7 + - - +
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A CYS* 3.8 6.3 - - - -
74A THR* 1.3 75.5 - - - +
76A VAL* 1.3 62.2 + - - +
77A SER* 3.9 20.8 - - - -
88A CYS* 3.3 3.3 - - - -
89A SER* 2.9 63.5 + - - -
90A SER 3.7 11.4 - - - -
92A PRO* 4.5 12.6 - - + +
101A ASN* 3.9 6.5 - - - +
103A ILE* 3.6 10.5 - - + +
104A GLU 3.1 30.3 - - - -
105A LYS* 4.1 11.2 - - - +
106A CYS* 3.6 26.2 - - - -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 3.4 27.8 - - + +
70A CYS* 3.5 23.1 - - - +
75A TYR* 1.3 76.9 - - - +
77A SER* 1.3 59.0 + - - +
78A GLU 3.5 28.2 + - - +
79A HIS* 3.7 12.3 - - + +
86A ARG* 4.6 3.8 - - + -
87A VAL 3.8 1.6 - - - +
101A ASN 4.0 2.2 - - - +
102A GLY* 3.6 33.9 - - - +
103A ILE 2.8 13.9 + - - +
104A GLU* 3.7 16.1 - - - +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.2 23.9 + - - -
76A VAL* 1.3 73.9 - - - +
78A GLU* 1.3 66.3 + - - +
87A VAL* 2.8 28.5 + - - +
89A SER* 3.1 27.5 + - - -
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Residues in contact with GLU 78 (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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76A VAL* 3.4 6.7 + - - +
77A SER* 1.3 86.5 + - - +
79A HIS* 1.3 67.8 + - - +
84A SER* 5.6 1.6 + - - -
85A LEU 5.4 1.6 - - - +
86A ARG* 3.3 4.6 - - - +
87A VAL* 2.9 54.5 + - + +
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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