Contacts of the helix formed by residues 125 - 133 (chain B) in PDB entry 3N56
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 ASN 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PHE 5.1 0.9 - - - -
116B LEU* 6.4 0.7 - - + -
123B LYS* 2.8 26.5 + - - +
124B GLU* 1.3 80.8 - - + +
126B GLU* 1.3 65.0 + - - +
127B TYR 3.1 3.5 + - - -
128B SER* 3.3 12.1 + - - +
129B GLN* 2.8 34.8 + - - +
817B GLU* 3.1 22.2 - - - +
821B ASN* 3.4 35.8 + - - +
825B THR* 5.9 0.4 - - + -
826B LYS* 5.8 1.8 - - - +
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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
----------------------------------------------------------
412A GLN* 3.2 29.7 + - + +
121B TYR* 3.8 33.7 - - + +
123B LYS* 2.8 48.3 + - + +
125B ASN* 1.3 76.5 - - - +
127B TYR* 1.3 57.3 + - - +
129B GLN* 4.1 6.2 - - - +
130B PHE* 2.9 36.6 + - - +
164B ARG* 2.9 34.3 + - + +
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Residues in contact with TYR 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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115B PHE* 3.6 36.0 + + + +
121B TYR* 6.0 0.2 - - - +
125B ASN 3.2 0.6 - - - -
126B GLU* 1.3 77.5 - - - +
128B SER* 1.3 71.5 + - - +
130B PHE* 3.2 6.6 + + + +
131B LEU* 3.2 39.0 + - + +
138B SER* 2.7 36.0 + - - -
151B PHE* 3.1 18.8 - + - +
161B ALA* 4.4 4.7 - - - -
164B ARG* 4.1 22.0 - - + +
165B PHE* 3.6 31.6 - + + -
168B PHE* 3.6 35.7 - + + -
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 5.3 4.7 + - - -
125B ASN* 3.3 18.7 + - - +
127B TYR* 1.3 87.7 - - - +
129B GLN* 1.3 56.7 + - - +
131B LEU* 3.5 6.3 + - - +
132B SER* 3.1 27.4 + - - -
138B SER* 6.4 0.2 - - - -
817B GLU* 3.6 16.8 + - - +
820B PHE* 5.1 11.4 - - - -
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS* 3.5 23.9 + - - +
125B ASN* 2.8 37.4 + - - +
126B GLU* 4.1 7.5 - - - +
128B SER* 1.3 71.1 - - - +
130B PHE* 1.3 65.3 + - - +
132B SER* 3.3 2.4 + - - -
133B GLU* 3.0 49.8 + - + +
817B GLU* 3.8 22.4 + - - +
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Residues in contact with PHE 130 (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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408A GLU* 4.2 4.9 - - - -
126B GLU* 2.9 24.3 + - - +
127B TYR* 3.2 4.9 + + - +
129B GLN* 1.3 77.0 + - - +
131B LEU* 1.3 71.6 + - + +
133B GLU* 4.8 4.0 - - - -
134B HIS* 2.8 58.5 + + - -
153B VAL* 4.5 6.1 - - + -
157B HIS* 4.1 17.3 - - + -
160B GLY* 3.7 6.1 - - - -
161B ALA* 3.3 36.8 - - + -
164B ARG* 3.4 48.9 - - - +
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Residues in contact with LEU 131 (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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127B TYR* 3.2 34.8 + - + +
128B SER* 3.8 7.6 - - - +
130B PHE* 1.3 76.5 - - + +
132B SER* 1.3 63.4 + - - +
134B HIS 2.9 9.4 + - - -
136B GLY* 2.7 38.2 + - - +
137B SER* 3.9 10.3 - - - +
138B SER* 3.4 33.0 - - - -
151B PHE* 4.0 6.7 - - + -
152B ASP 3.8 15.3 - - - +
153B VAL* 3.9 15.7 - - + -
161B ALA* 4.0 19.3 - - + -
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Residues in contact with SER 132 (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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128B SER 3.1 14.2 + - - -
129B GLN* 3.3 5.6 + - - -
131B LEU* 1.3 76.3 - - - +
133B GLU* 1.3 62.2 - - - +
134B HIS 3.4 0.3 + - - -
135B ALA 3.7 2.3 + - - -
136B GLY 4.2 3.8 + - - -
813B GLN* 3.2 29.8 + - - -
816B SER* 4.7 4.0 + - - -
817B GLU* 3.4 36.4 + - - +
818B PRO* 5.5 0.2 - - - +
885B HIS* 5.0 3.5 + - - -
892B ARG* 3.3 20.1 + - - +
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Residues in contact with GLU 133 (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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415A LYS* 5.5 0.9 + - - -
129B GLN* 3.0 47.4 + - + +
130B PHE* 3.9 5.5 - - - +
132B SER* 1.3 76.8 - - - +
134B HIS* 1.3 74.8 + - + +
135B ALA 3.6 0.7 - - - -
881B ALA* 5.9 3.6 - - - -
884B LYS* 3.5 53.5 + - + +
885B HIS* 3.7 34.8 + - + +
888B ALA* 3.8 5.5 - - - +
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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