Contacts of the helix formed by residues 117 - 123 (chain B) in PDB entry 2AG1
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 ASP 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PRO* 4.3 15.0 + - + +
115B GLY 4.1 1.4 + - - -
116B ILE* 1.3 66.6 - - - +
118B GLN* 1.3 62.8 + - - +
119B VAL* 3.6 8.3 + - - +
120B ALA* 3.0 34.8 + - + +
121B MSE 3.1 27.2 + - - +
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Residues in contact with GLN 118 (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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74B ALA* 3.7 5.9 - - - +
75B GLY* 2.7 38.4 - - - +
78B PHE* 3.3 50.8 - - + +
99B THR* 3.8 4.7 + - - +
100B GLY 2.9 19.7 + - - +
101B SER* 3.5 7.2 - - - -
113B GLN 4.5 2.6 + - - -
116B ILE* 2.9 27.9 + - + +
117B ASP* 1.3 72.0 + - - +
119B VAL* 1.3 61.9 - - - +
121B MSE 3.1 2.5 + - - -
122B ALA* 3.1 19.9 + - - +
158B LEU* 4.4 3.8 - - + -
160B ASP* 2.9 21.5 + - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 3.3 6.8 + - - +
118B GLN* 1.3 76.9 - - - +
120B ALA* 1.3 57.5 + - - +
122B ALA* 3.2 1.9 + - - +
123B ALA* 2.9 31.5 + - + +
129B ALA* 3.5 26.5 - - + +
130B HIS* 3.8 28.7 - - - +
131B ARG* 3.8 19.3 - - + +
158B LEU* 4.4 8.7 - - + -
160B ASP* 3.9 15.0 + - + +
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Residues in contact with ALA 120 (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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120A ALA 4.5 5.5 - - - +
124A PRO* 3.9 15.9 - - + -
117B ASP* 3.0 38.8 + - + +
119B VAL* 1.3 77.8 - - - +
121B MSE 1.3 62.0 + - - +
123B ALA* 3.6 7.5 + - - +
124B PRO* 3.4 18.0 - - - +
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Residues in contact with MSE 121 (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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82A VAL* 4.7 6.7 - - + -
121A MSE 3.5 40.7 - - + +
124A PRO* 4.0 10.1 - - + -
125A ILE* 4.0 30.5 - - + -
78B PHE* 3.9 19.3 - - + -
79B THR* 4.5 9.2 - - - -
82B VAL* 5.5 5.0 - - + +
116B ILE* 3.4 41.7 - - + -
117B ASP 3.1 26.4 + - - +
118B GLN* 3.1 13.2 + - - +
120B ALA* 1.3 80.2 - - - +
122B ALA* 1.3 55.2 + - - +
124B PRO* 3.2 12.5 - - - +
125B ILE* 4.4 4.0 - - - +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 4.1 10.8 - - + -
82B VAL* 6.3 0.4 - - - -
85B ILE* 4.7 6.1 - - + -
118B GLN 3.1 14.8 + - - +
119B VAL 4.0 1.8 - - - +
121B MSE 1.3 72.7 - - - +
123B ALA* 1.3 61.1 + - - +
124B PRO* 3.2 3.8 - - - -
125B ILE* 3.0 20.8 + - - +
126B THR* 2.6 39.6 + - + +
129B ALA* 4.4 1.3 - - + -
158B LEU* 3.9 23.1 - - + -
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Residues in contact with ALA 123 (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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89B TRP* 5.9 0.2 - - - -
119B VAL* 2.9 19.3 + - + +
120B ALA* 3.9 7.6 - - - +
122B ALA* 1.3 76.9 - - - +
124B PRO* 1.4 63.5 - - + +
125B ILE 3.0 5.4 + - - -
126B THR* 3.7 18.9 + - - +
129B ALA* 4.3 7.2 - - + +
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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