Contacts of the strand formed by residues 95 - 101 (chain H) in PDB entry 1OZT
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 ALA 95 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H SER* 3.1 6.8 - - - -
35H ILE* 2.7 41.6 + - + +
38H LEU* 4.1 15.9 - - + -
87H VAL* 4.4 17.0 - - + -
88H THR 3.2 24.9 - - - +
89H ALA* 4.0 3.1 - - - -
93H GLY 4.1 0.2 + - - -
94H VAL* 1.3 76.3 - - - +
96H ASP* 1.3 60.4 + - - +
97H VAL* 3.6 3.2 + - + +
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Residues in contact with ASP 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H GLY 3.9 2.9 - - - +
34H SER* 3.9 15.0 - - - -
87H VAL* 5.8 0.2 - - - +
88H THR 4.1 8.0 + - - +
94H VAL* 4.1 10.5 + - + +
95H ALA* 1.3 74.1 - - - +
97H VAL* 1.3 64.3 + - - +
98H SER* 4.0 1.6 + - - -
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Residues in contact with VAL 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ILE* 4.2 14.6 - - + -
31H VAL* 4.0 22.2 - - + +
32H TRP* 3.1 7.1 - - - +
33H GLY 2.7 42.5 + - - +
35H ILE* 4.4 7.2 - - + -
45H PHE* 4.3 4.9 - - + -
87H VAL* 3.5 31.9 - - + -
95H ALA 4.0 9.2 - - - +
96H ASP* 1.3 79.1 - - - +
98H SER* 1.3 64.8 + - - +
99H ILE* 4.1 21.5 - - + -
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Residues in contact with SER 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H VAL 3.5 4.3 - - - -
32H TRP* 4.2 8.1 - - - +
96H ASP 4.0 2.5 + - - -
97H VAL* 1.3 78.2 - - - +
99H ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H LYS* 3.6 4.0 - - - +
31H VAL* 2.9 43.4 + - + +
45H PHE* 4.0 32.5 - - + -
84H LEU* 4.0 21.8 - - + +
86H ASN 4.7 10.3 - - - +
87H VAL* 4.9 1.3 - - + -
97H VAL* 4.1 11.0 - - + -
98H SER* 1.3 80.8 + - - +
100H GLU* 1.3 84.0 - - - +
101H ASP* 4.3 9.0 - - + +
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Residues in contact with GLU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H PRO* 3.9 30.7 - - + +
29H VAL 3.5 7.4 - - - +
30H LYS* 3.9 28.2 - - + +
99H ILE* 1.3 81.2 - - - +
101H ASP* 1.3 63.2 + - - +
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Residues in contact with ASP 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H PRO* 4.3 2.2 - - - -
29H VAL* 2.8 36.7 + - - +
31H VAL* 5.0 0.9 - - + +
79H ARG* 2.6 31.2 + - - -
84H LEU* 3.6 24.0 - - + +
99H ILE* 4.2 7.3 - - + +
100H GLU* 1.3 76.1 - - - +
102H SER* 1.3 60.0 + - - +
103H VAL* 2.5 33.4 + - - +
104H ILE* 3.0 24.3 + - + +
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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
------------------------------------------------------------
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