Contacts of the strand formed by residues 125 - 129 (chain B) in PDB entry 1O69
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 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 4.2 13.7 - - + -
67B ALA* 5.0 2.2 - - + -
69B VAL* 4.4 9.6 - - + -
74B ILE 4.0 2.1 + - - +
75B VAL* 3.6 6.6 - - + -
76B LEU* 2.9 28.2 + - - +
123B PRO* 3.5 1.7 - - - +
124B LYS* 1.3 80.4 - - - +
126B LEU* 1.3 58.5 + - - +
150B ILE* 3.5 8.2 - - - +
151B VAL* 3.2 18.6 - - + +
153B ILE* 4.1 21.1 - - + -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 3.3 29.6 - - + +
99B ILE* 4.6 0.2 - - + -
107B ILE* 3.7 28.7 - - + -
112B LEU* 4.2 19.3 - - + -
125B ALA* 1.3 73.9 - - - +
127B ILE* 1.3 71.0 + - - +
128B LEU* 4.1 7.0 - - + +
141B ILE* 3.9 19.5 - - + -
145B CYS* 3.8 23.6 - - - -
150B ILE* 3.5 12.3 - - + +
151B VAL 2.9 8.1 + - - +
152B LEU* 3.9 7.4 - - + +
153B ILE* 2.8 31.5 + - - +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.2 14.8 - - + -
64B LEU* 4.0 26.5 - - + -
75B VAL* 4.1 6.5 - - + -
76B LEU 2.9 12.2 + - - +
77B ALA* 3.4 6.3 - - + -
78B SER* 3.2 26.0 + - - -
85B SER* 3.6 32.8 - - - +
86B VAL* 4.8 3.6 - - + -
88B PRO* 5.5 0.4 - - + -
89B ILE* 3.9 32.3 - - + +
126B LEU* 1.3 73.8 - - - +
128B LEU* 1.3 60.1 + - - +
129B THR* 3.8 2.0 + - - +
153B ILE* 3.4 12.6 - - + +
155B ASP* 4.0 22.0 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B SER* 3.7 1.3 - - - -
107B ILE* 3.9 33.9 - - + +
126B LEU* 3.6 6.4 + - + -
127B ILE* 1.3 72.6 - - - +
129B THR* 1.3 72.7 + - - +
130B HIS* 3.8 11.9 + - + +
136B ALA* 4.0 15.0 - - + -
138B MET* 3.7 37.0 - - + -
141B ILE* 4.0 21.3 - - + -
152B LEU* 4.0 17.7 - - + -
153B ILE 2.9 10.2 + - - +
154B GLU* 3.6 5.7 - - + -
155B ASP* 2.8 24.9 + - - +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B SER* 2.8 24.5 + - - -
80B PHE 4.6 1.1 - - - -
81B THR* 2.8 25.8 + - - +
85B SER* 4.1 3.3 - - - -
106B ASN* 3.0 22.3 - - - +
127B ILE* 3.8 2.8 + - - +
128B LEU* 1.3 79.3 - - - +
130B HIS* 1.3 64.7 + - - +
131B LEU* 3.6 30.1 - - + +
155B ASP* 2.7 31.9 + - - +
395B X04 3.7 9.0 - - + -
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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