Contacts of the strand formed by residues 125 - 129 (chain H) in PDB entry 6CMO
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 125 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H GLU* 4.5 18.4 - - + -
10H SER 5.9 1.1 - - - +
12H GLY* 4.5 23.7 - - - +
13H GLY 5.2 0.7 + - - -
23H LEU* 5.9 2.9 - - + -
39H TRP* 6.4 1.1 - - + -
96H VAL* 3.4 8.5 - - - +
97H TYR* 3.2 33.4 + - + +
124H GLY* 1.3 74.8 - - - -
126H LEU* 1.3 67.9 + - - +
127H VAL* 3.8 5.1 + - + -
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Residues in contact with LEU 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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13H GLY* 3.6 14.6 + - - +
14H LEU* 4.2 16.7 - - + +
44H PRO* 6.1 2.9 - - + -
94H THR* 4.6 11.2 - - + -
95H ALA* 4.1 4.3 - - - +
96H VAL* 3.8 24.7 - - + +
125H THR* 1.3 80.8 + - - +
127H VAL* 1.3 83.4 + - - +
128H THR* 4.8 4.7 - - + +
166H GLU* 4.3 24.5 - - + +
167H PRO* 4.5 12.1 - - + -
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Residues in contact with VAL 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H GLY* 4.4 4.0 - - - -
13H GLY 3.5 24.0 - - - +
15H VAL* 3.9 8.3 - - + -
23H LEU* 4.3 17.7 - - + -
86H MET* 3.8 25.6 - - + -
89H LEU* 5.2 4.3 - - + -
93H ASP 4.5 2.4 - - - +
94H THR* 3.6 4.0 - - - +
95H ALA 3.0 33.1 + - - +
97H TYR* 3.7 32.3 - - + +
125H THR* 3.8 5.8 + - + +
126H LEU* 1.3 80.6 - - - +
128H THR* 1.3 64.8 + - - +
129H VAL* 5.7 0.9 - - + -
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Residues in contact with THR 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H GLY 4.1 2.8 + - - -
14H LEU* 3.7 34.9 - - + +
15H VAL* 3.1 34.4 + - - +
94H THR* 3.0 23.0 + - - +
126H LEU* 4.3 6.9 - - + -
127H VAL* 1.3 76.4 - - - +
129H VAL* 1.3 77.4 + - - +
130H SER* 4.5 10.2 - - - +
164H PHE* 6.1 3.8 - - + -
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Residues in contact with VAL 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H VAL* 3.5 3.8 - - + +
16H GLN 4.7 0.4 - - - +
17H PRO* 3.7 32.1 - - + -
89H LEU* 3.7 28.9 - - + -
90H ARG* 3.4 32.8 - - - +
91H ALA* 3.8 21.0 - - + +
93H ASP* 4.3 12.8 - - + +
94H THR* 2.8 18.9 + - - +
127H VAL* 5.7 1.1 - - + -
128H THR* 1.3 78.9 + - - +
130H SER* 1.3 64.1 + - - +
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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