Contacts of the strand formed by residues 122 - 126 (chain H) in PDB entry 3HO5
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 LEU 122 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H ASP 4.0 3.0 + - - +
84H ILE* 3.3 19.4 - - + +
85H ILE* 3.0 23.3 + - - +
106H LEU* 3.7 46.7 - - + +
109H LEU* 3.8 25.1 - - + -
110H ALA* 4.1 18.7 + - + +
113H VAL* 3.9 11.6 - - + +
121H LYS* 1.3 73.4 - - - +
123H ARG* 1.3 61.4 + - - +
124H VAL* 5.1 0.2 - - + -
148H ILE* 3.9 17.9 - - + -
149H THR 3.9 3.6 - - - +
150H THR* 4.9 0.4 - - - +
161H LEU* 3.7 28.9 - - + -
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Residues in contact with ARG 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLU* 3.1 29.5 + - - -
85H ILE* 3.2 29.5 - - + +
87H LYS* 3.3 30.8 - - - +
121H LYS 3.6 0.4 + - - -
122H LEU* 1.3 73.9 - - - +
124H VAL* 1.3 67.9 + - - +
125H THR* 3.7 8.6 - - - +
148H ILE* 3.3 6.8 - - - +
149H THR* 2.7 76.0 + - - +
150H THR 3.8 15.5 - - - -
151H SER* 3.9 17.5 + - - +
153H ARG* 3.5 33.8 - - - +
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Residues in contact with VAL 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H ILE* 3.8 21.1 - - + -
85H ILE 2.6 9.4 + - - +
86H PHE* 3.6 31.2 - - + -
87H LYS* 2.7 34.5 + - - +
95H ASP* 4.0 10.4 - - + +
106H LEU* 4.1 15.7 - - + -
122H LEU* 5.1 1.1 - - + -
123H ARG* 1.3 78.5 - - - +
125H THR* 1.3 60.9 + - - +
126H GLU 3.4 28.0 - - - +
127H GLY* 4.8 0.7 - - - -
146H VAL* 4.8 3.8 - - + -
147H ASP 3.7 3.4 - - - +
148H ILE* 4.3 13.5 - - + -
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Residues in contact with THR 125 (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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380B GLU* 3.1 56.5 + - + +
381B GLU* 4.1 3.9 - - - +
87H LYS* 3.8 13.7 - - + -
89H GLU* 3.3 5.9 - - - +
95H ASP* 2.9 6.8 - - - +
123H ARG* 3.7 18.4 - - - +
124H VAL* 1.3 73.5 - - - +
126H GLU* 1.3 56.3 + - - +
147H ASP* 2.8 27.1 + - - +
148H ILE* 4.8 0.2 - - - -
149H THR* 4.4 9.2 - - + +
180H HIS* 4.5 2.6 - - - +
401H CA 2.4 30.3 - - - -
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Residues in contact with GLU 126 (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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381B GLU* 3.3 34.3 - - - +
89H GLU* 3.9 3.4 - - - -
90H GLU* 2.5 2.1 - - - +
95H ASP* 2.8 7.4 - - - +
124H VAL* 3.4 13.3 - - - +
125H THR* 1.3 82.9 + - - +
127H GLY* 1.3 57.9 + - - +
128H TRP 4.6 0.3 - - - +
129H ASP* 2.8 14.1 - - - +
133H HIS* 4.4 2.1 + - - +
134H HIS* 3.0 19.1 + - + +
140H HIS* 4.1 2.9 - - + +
146H VAL* 3.3 3.9 - - - -
147H ASP* 2.8 42.8 + - + +
401H CA 2.3 25.3 - - - -
402H CA 2.3 30.1 - - - -
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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