Contacts of the strand formed by residues 123 - 127 (chain B) in PDB entry 3N1G
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 123 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASP 3.9 6.8 + - - +
85B ILE* 3.6 15.7 - - + -
86B ILE* 2.9 25.9 + - - +
107B VAL* 3.4 38.6 - - + +
110B LEU* 3.9 31.4 - - + -
111B ALA* 4.4 11.4 - - - +
114B VAL* 3.7 16.6 - - + +
122B ARG* 1.3 75.4 - - - +
124B ARG* 1.3 68.0 + - - +
125B VAL* 4.7 2.7 - - + -
149B ILE* 3.9 20.9 - - + -
150B THR 3.9 11.0 - - - +
151B THR* 4.9 0.2 - - - +
162B LEU* 4.0 11.9 - - + -
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 3.4 23.1 - - + +
88B LYS* 3.8 11.4 - - - +
123B LEU* 1.3 75.1 - - - +
125B VAL* 1.3 70.8 + - - +
126B THR* 3.6 17.7 - - - +
149B ILE* 3.1 8.3 - - - +
150B THR* 2.9 67.5 + - - +
151B THR 4.0 9.0 - - - +
152B SER* 4.2 3.4 - - - +
154B ARG* 3.3 40.9 - - - +
755C THR* 3.0 23.0 + - - +
756C ASP* 3.9 4.0 + - - -
758C ASP* 2.8 40.5 + - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.7 22.9 - - + -
86B ILE 2.8 8.3 + - - -
87B PHE* 3.7 27.3 - - + -
88B LYS* 2.8 29.1 + - - +
96B ASP* 4.0 7.4 - - + +
107B VAL* 4.9 1.1 - - + -
123B LEU* 4.7 4.3 - - + -
124B ARG* 1.3 76.8 - - - +
126B THR* 1.3 62.5 + - - +
127B GLU 3.6 28.3 - - - +
128B GLY 4.0 3.4 - - - +
147B LEU* 4.3 20.2 - - + -
148B ASP 3.4 4.7 - - - +
149B ILE* 4.2 12.8 - - + -
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Residues in contact with THR 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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88B LYS* 3.7 14.4 - - + +
90B GLU* 3.5 6.1 - - - +
96B ASP* 3.2 3.6 - - - +
124B ARG* 3.6 39.5 + - + +
125B VAL* 1.3 73.7 - - - +
127B GLU* 1.3 59.8 + - - +
148B ASP* 2.8 31.8 + - - +
149B ILE 4.3 0.2 + - - -
150B THR* 4.2 13.9 - - + -
181B HIS* 4.7 5.6 - - + +
191B CA 2.4 28.6 - - - -
755C THR* 4.5 13.2 - - + -
806C ILE* 4.2 3.9 - - - +
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Residues in contact with GLU 127 (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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90B GLU* 3.2 2.4 - - - +
91B GLU* 2.9 0.9 - - - +
96B ASP* 3.3 2.6 - - - +
125B VAL* 3.6 7.1 - - - +
126B THR* 1.3 81.2 + - - +
128B GLY* 1.3 59.6 + - - +
130B ASP* 3.2 4.9 - - - +
134B HIS* 3.1 12.7 + - + -
135B HIS* 2.6 33.7 + - + +
141B HIS* 3.7 10.3 - - + +
147B LEU* 3.2 5.7 - - - -
148B ASP* 2.8 45.0 + - + +
190B CA 2.6 27.1 - - - -
191B CA 2.4 27.9 - - - -
806C ILE* 3.6 16.6 - - + -
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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