Contacts of the strand formed by residues 97 - 104 (chain Z) in PDB entry 3SDI
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 97 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45Z ALA* 3.4 34.5 - - + +
46Z ASN 3.3 10.8 - - - +
47Z GLY* 4.5 0.2 - - - -
48Z PHE 3.7 7.9 - - - +
51Z ASP* 4.3 1.6 - - + -
52Z GLY* 3.6 21.5 - - - +
55Z LEU* 4.2 6.7 - - + -
87Z LEU* 4.7 3.0 - - + +
95Z TYR* 2.8 29.8 + - + +
96Z TYR* 1.3 78.9 - - - +
98Z HIS* 1.3 63.2 + - - +
99Z THR* 3.8 17.4 + - - +
114Z ASP 4.3 0.5 - - - -
115Z PRO* 3.4 28.5 - - - +
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Residues in contact with HIS 98 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Z ILE* 3.7 9.7 - - + +
45Z ALA* 3.6 0.7 - - - -
46Z ASN 2.7 37.3 + - - +
97Z VAL* 1.3 71.7 - - - +
99Z THR* 1.3 60.9 + - - +
100Z ILE* 5.3 1.6 - - + -
113Z PHE 4.1 10.1 + - - +
114Z ASP* 4.9 1.6 - - + -
115Z PRO* 4.1 25.3 - - + +
127Z GLY* 4.5 8.7 - - - -
128Z GLY* 3.7 35.8 + - - +
131Z ALA* 5.9 1.9 - - + +
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Residues in contact with THR 99 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Z MET* 3.7 33.4 - - + -
44Z SER 3.3 12.1 - - - +
45Z ALA* 3.9 2.9 - - + +
55Z LEU* 3.5 21.7 - - + +
83Z ILE* 4.6 2.9 - - + -
87Z LEU* 4.4 7.2 - - - +
97Z VAL* 3.8 11.5 + - - +
98Z HIS* 1.3 75.2 - - - +
100Z ILE* 1.3 66.4 + - - +
101Z ILE* 4.6 1.6 - - + -
112Z SER* 3.3 4.0 - - - -
113Z PHE* 2.8 58.7 + - + +
114Z ASP 5.4 0.2 + - - -
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Residues in contact with ILE 100 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Z ILE* 3.5 33.4 - - + +
4Z LEU 4.7 0.4 - - - +
5Z GLY* 4.6 7.6 - - - +
14Z LEU* 3.5 21.1 - - + +
44Z SER 3.0 32.0 + - - +
98Z HIS* 4.1 2.2 + - + -
99Z THR* 1.3 80.1 - - - +
101Z ILE* 1.3 70.9 + - - +
110Z VAL* 3.9 21.8 - - + -
111Z TYR 3.4 10.5 - - - +
112Z SER* 3.9 2.9 - - - -
113Z PHE* 5.0 0.2 - - - -
125Z ARG* 3.6 40.6 - - + +
126Z ALA 4.1 0.2 - - - -
127Z GLY* 3.9 9.9 - - - +
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Residues in contact with ILE 101 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Z LEU* 4.5 0.4 - - - -
41Z ILE* 4.4 6.5 - - + -
42Z VAL 3.2 9.9 - - - +
43Z MET* 3.7 18.4 - - + -
76Z ILE* 4.0 24.0 - - + +
79Z ALA* 4.0 5.4 - - + -
80Z ALA* 3.8 34.3 - - + +
83Z ILE* 3.6 29.6 - - + -
99Z THR* 4.6 1.6 - - + -
100Z ILE* 1.3 82.9 - - - +
102Z ALA* 1.3 62.2 + - - +
109Z ALA 3.9 0.2 - - - +
110Z VAL* 3.3 4.3 - - - -
111Z TYR* 2.9 46.1 + - + +
113Z PHE* 4.2 7.2 - - + -
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Residues in contact with ALA 102 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z ALA* 3.9 16.8 - - + -
13Z VAL 4.4 3.6 - - - +
14Z LEU* 4.2 14.3 - - + +
40Z ASN 4.0 0.2 - - - +
41Z ILE* 3.6 1.0 - - - -
42Z VAL* 3.0 48.8 + - + +
76Z ILE* 3.5 10.8 - - - +
100Z ILE* 5.6 0.2 - - + -
101Z ILE* 1.3 76.2 - - - +
103Z GLY* 1.3 58.4 - - - +
109Z ALA 3.1 10.5 - - - +
110Z VAL* 4.3 8.5 - - + -
178Z VAL* 4.5 0.8 - - + +
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Residues in contact with GLY 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z ALA* 3.7 6.6 - - - +
40Z ASN 3.7 15.5 - - - -
76Z ILE* 3.7 8.4 - - - +
102Z ALA* 1.3 76.1 - - - +
104Z LEU* 1.3 65.8 + - - +
108Z GLY* 3.6 3.8 - - - -
109Z ALA* 2.8 30.9 + - - -
178Z VAL* 4.0 11.9 - - - -
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Residues in contact with LEU 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Z ASP 3.8 24.2 - - - +
11Z PHE* 3.9 11.0 - - - +
40Z ASN* 4.1 14.8 + - - +
73Z LYS* 5.7 7.6 + - - +
75Z SER* 5.7 0.7 - - - -
76Z ILE* 3.5 18.7 + - - +
103Z GLY* 1.3 78.9 - - - +
105Z ASP* 1.3 69.2 + - - +
106Z GLY* 3.6 25.4 - - + +
107Z LYS 3.2 10.8 - - - +
108Z GLY* 4.2 0.7 - - - -
178Z VAL* 4.0 9.4 - - + +
179Z THR* 3.7 5.6 - - - +
180Z LYS* 3.5 34.8 - - + +
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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