Contacts of the strand formed by residues 123 - 126 (chain B) in PDB entry 6DMY
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 ARG 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A GLU* 3.3 8.9 + - - -
951A ASP* 3.9 6.1 + - - -
954A ASP* 4.9 7.5 + - - -
956A MET* 5.5 3.7 - - - +
85B ILE* 3.3 35.1 - - + +
87B LYS* 3.4 34.7 - - - +
121B LYS 3.2 2.1 + - - +
122B LEU* 1.3 70.3 - - - +
124B VAL* 1.3 63.9 + - - +
125B THR* 3.4 18.3 + - - +
148B ILE* 3.3 3.1 - - - -
149B THR* 2.6 62.1 + - - +
150B THR 3.3 23.8 - - - +
151B SER* 4.4 5.6 - - - +
153B ARG* 3.1 44.2 - - - +
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Residues in contact with VAL 124 (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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84B ILE* 3.9 12.3 - - + -
85B ILE 3.1 6.0 + - - +
86B PHE* 3.6 24.2 - - + -
87B LYS 3.3 20.7 + - - -
95B ASP* 4.5 6.6 - - + +
98B MET* 5.0 0.4 - - + -
106B LEU* 3.8 37.0 - - + -
122B LEU* 3.6 3.4 + - + +
123B ARG* 1.3 71.4 - - - +
125B THR* 1.3 64.2 + - - +
126B GLU 4.3 9.6 - - - +
127B GLY 4.8 0.2 - - - +
146B VAL* 4.0 23.8 - - + -
147B ASP 3.4 9.4 - - - +
148B ILE* 4.0 9.6 - - + -
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Residues in contact with THR 125 (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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212A GLU* 4.9 10.0 + - + +
87B LYS* 3.9 17.9 - - - +
89B GLU* 3.4 4.7 - - - +
95B ASP* 2.9 13.2 - - - +
123B ARG* 3.4 33.7 - - - +
124B VAL* 1.3 75.8 - - - +
126B GLU* 1.3 69.3 + - - +
147B ASP* 2.8 30.6 + - - +
148B ILE 4.9 0.2 - - - -
149B THR* 4.1 19.5 - - + +
180B HIS* 4.9 6.3 - - + +
204B CA 2.5 21.6 - - - -
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Residues in contact with GLU 126 (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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212A GLU 3.8 18.4 - - - +
213A THR* 4.4 10.0 - - - +
214A GLY* 4.6 6.8 - - - -
87B LYS* 5.5 3.2 + - + +
89B GLU* 3.8 9.8 - - - +
124B VAL* 3.7 3.3 - - - -
125B THR* 1.3 91.5 + - - +
127B GLY* 1.3 59.9 + - - +
129B ASP* 5.9 2.2 - - + -
134B HIS* 3.1 35.3 - - + +
140B HIS* 3.7 5.5 - - + +
146B VAL* 3.4 4.5 - - - +
147B ASP* 3.0 40.2 + - - +
180B HIS* 5.6 1.5 + - - -
204B CA 3.0 20.0 - - - -
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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