Contacts of the strand formed by residues 101 - 106 (chain Y) in PDB entry 3HI6
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 101 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y GLN* 3.2 19.3 + - - +
8Y PRO* 2.5 28.3 + - + +
9Y SER 3.2 7.4 - - - +
10Y SER* 4.2 4.3 - - - -
11Y LEU* 4.1 19.7 - - + -
21Y ILE* 3.4 33.8 - - + +
84Y ALA 3.7 0.3 - - - +
85Y THR* 3.3 5.0 - - - +
86Y TYR* 2.9 37.9 + - - +
100Y GLY* 1.3 70.9 - - - -
102Y LYS* 1.3 65.5 + - - +
103Y VAL* 3.6 2.4 + - + -
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Residues in contact with LYS 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y SER 2.9 15.0 + - - +
10Y SER* 3.2 11.0 - - - -
11Y LEU 3.0 26.3 + - - +
84Y ALA 3.8 4.7 - - - +
85Y THR* 3.4 22.0 - - + +
100Y GLY 4.3 0.2 - - - -
101Y THR* 1.3 71.6 - - - +
103Y VAL* 1.3 62.6 + - - +
104Y GLU* 3.8 1.1 + - - +
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Residues in contact with VAL 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Y LEU* 3.5 33.2 - - + -
19Y VAL* 4.8 4.3 - - + -
21Y ILE* 4.3 12.3 - - + -
75Y ILE* 5.1 1.8 - - + -
78Y LEU* 4.0 28.7 - - + -
82Y ASP 4.3 5.8 - - - +
83Y PHE* 3.3 20.3 - - - -
84Y ALA 2.9 19.9 + - - +
86Y TYR* 3.7 30.5 - - + -
101Y THR* 4.4 1.6 - - + +
102Y LYS* 1.3 74.3 - - - +
104Y GLU* 1.3 70.4 + - - +
105Y ILE* 4.9 2.2 - - + -
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Residues in contact with GLU 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Y LEU 2.8 10.4 + - - +
12Y SER* 3.2 34.0 + - - +
13Y ALA 3.2 23.9 + - - +
83Y PHE* 4.1 5.6 - - + -
102Y LYS 3.8 1.5 + - - +
103Y VAL* 1.3 79.7 - - - +
105Y ILE* 1.3 63.2 + - - +
139Y TYR* 3.2 24.1 + - - -
165Y GLN* 3.6 10.8 - - - +
172Y TYR* 2.9 26.0 + - - +
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Residues in contact with ILE 105 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Y SER* 4.3 0.4 - - - -
13Y ALA 3.5 4.5 - - - +
15Y VAL* 4.2 20.6 - - + -
78Y LEU* 3.7 26.9 - - + -
79Y GLN 3.9 19.1 - - - +
80Y LEU* 4.3 11.7 - - + +
83Y PHE* 4.2 27.1 - - + +
103Y VAL* 4.9 0.9 - - + -
104Y GLU* 1.3 72.6 - - - +
106Y LYS* 1.3 73.0 + - - +
107Y ARG* 3.7 2.7 + - + -
139Y TYR* 3.6 7.0 + - - -
165Y GLN* 2.4 41.7 + - - +
170Y SER* 3.5 23.9 - - - +
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Residues in contact with LYS 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y SER* 3.4 28.7 + - - +
13Y ALA* 2.9 16.8 + - - +
14Y SER* 3.4 43.5 + - - +
15Y VAL 4.3 0.9 + - - -
17Y ASP* 4.5 6.0 + - - -
104Y GLU 3.7 1.8 + - - -
105Y ILE* 1.3 76.9 - - - +
107Y ARG* 1.3 69.3 + - - +
139Y TYR* 3.3 15.0 - - + +
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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