Contacts of the strand formed by residues 101 - 106 (chain A) in PDB entry 3SA0
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 VAL 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LYS* 3.8 0.7 - - - -
56A ILE* 2.7 45.9 + - + +
58A PRO* 5.3 2.2 - - + -
59A PHE* 4.0 24.2 - - + -
68A THR* 5.9 1.6 - - + -
72A ILE* 5.0 6.7 - - + -
89A ILE* 3.3 29.4 - - + -
90A ILE 3.6 5.6 - - - +
91A ARG* 4.3 4.5 - - + -
98A MET* 4.1 14.6 - - - -
100A ASP* 1.3 80.1 - - - +
102A TYR* 1.3 65.5 + - - +
103A ILE* 4.4 8.7 - - + -
347A ILE* 4.3 9.6 - - + -
351A THR* 4.7 7.2 - - + -
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Residues in contact with TYR 102 (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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18A VAL* 3.6 12.3 + - - +
19A PHE* 4.1 19.1 - + - -
20A ASP* 2.9 42.4 + - - -
21A VAL* 3.4 20.9 - - + -
53A ILE* 3.8 12.1 - - + -
54A LYS 3.2 3.1 - - - -
55A LYS* 3.5 43.8 - - + -
88A ASP 3.9 0.3 - - - +
89A ILE* 3.2 7.4 - - - +
90A ILE* 2.8 62.8 + - + +
91A ARG* 5.6 0.7 - - - -
100A ASP* 4.4 16.9 + - + -
101A VAL* 1.3 75.0 - - - +
103A ILE* 1.3 62.0 + - - +
104A VAL 4.0 0.4 + - - -
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ALA 3.9 0.3 - - - +
53A ILE* 3.3 2.2 - - - -
54A LYS* 2.8 57.1 + - + +
56A ILE* 4.1 22.9 - - + -
68A THR* 5.4 2.2 - - + -
71A GLU* 5.1 6.1 - - + +
72A ILE* 4.1 29.6 - - + -
86A ILE* 3.9 31.9 - - + -
88A ASP 3.7 2.9 - - - -
89A ILE* 4.7 6.3 - - + +
101A VAL* 4.4 10.1 - - + -
102A TYR* 1.3 76.5 - - - +
104A VAL* 1.3 62.4 + - - +
105A GLN* 4.0 19.5 + - + +
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Residues in contact with VAL 104 (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 TYR* 3.8 27.8 - - + +
44A ASP* 5.5 0.7 - - - +
51A VAL* 3.7 28.3 - - + -
52A ALA 3.3 10.5 - - - +
53A ILE* 4.0 12.8 - - + +
86A ILE* 3.7 1.6 - - - -
87A ASN* 2.8 40.0 + - + -
88A ASP* 2.9 35.5 + - + +
90A ILE* 4.1 12.8 - - + -
102A TYR 4.7 0.2 - - - +
103A ILE* 1.3 73.9 - - - +
105A GLN* 1.3 62.6 + - - +
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Residues in contact with GLN 105 (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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51A VAL* 3.5 6.8 - - - +
52A ALA* 2.8 26.3 + - + +
54A LYS* 3.4 22.2 + - + +
71A GLU* 5.4 0.8 + - - -
75A LEU* 3.9 15.6 - - - +
84A ILE* 3.8 23.8 - - + +
85A GLY 3.3 25.5 + - - +
86A ILE* 4.1 5.5 - - - +
87A ASN* 3.6 9.6 - - - +
103A ILE* 4.0 14.4 - - + +
104A VAL* 1.3 79.2 - - - +
106A ASP* 1.3 66.1 + - - +
107A LEU 3.4 0.2 + - - -
156A LEU* 5.5 0.2 - - - +
166A CME 5.8 1.0 - - - +
361A NRA 2.8 44.7 + - + +
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Residues in contact with ASP 106 (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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51A VAL* 5.1 2.9 - - - +
84A ILE* 4.2 12.9 - - + +
85A GLY* 4.8 3.8 + - - -
87A ASN* 3.1 25.7 + - - +
105A GLN* 1.3 75.4 - - - +
107A LEU* 1.3 54.6 + - - +
108A MET* 3.5 13.4 + - - +
164A LYS* 4.0 18.4 + - - +
361A NRA 2.4 30.7 + - - -
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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