Contacts of the helix formed by residues 81 - 92 (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 ALA 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B GLU* 4.5 6.3 - - + +
54B GLY* 5.7 0.4 - - - -
72B VAL* 4.3 22.0 - - + -
77B GLY 3.5 10.1 + - - +
78B PHE* 2.8 14.6 + - + +
80B ASN* 1.3 78.7 - - - +
82B VAL* 1.3 63.3 + - - +
83B THR 3.4 1.3 - - - -
84B PRO* 3.1 19.2 - - - +
85B ILE* 3.2 21.1 + - + +
97B PHE* 4.6 15.7 - - + -
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Residues in contact with VAL 82 (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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79A THR* 4.2 23.8 - - + +
82A VAL* 4.5 20.9 - - + -
121A MSE 4.7 5.6 - - + -
78B PHE* 3.9 36.6 - - + +
79B THR* 3.3 17.7 + - - +
80B ASN 3.3 2.8 - - - -
81B ALA* 1.3 77.4 - - - +
83B THR* 1.3 64.0 + - - +
85B ILE* 3.1 10.1 + - + +
86B ALA* 2.9 21.0 + - - +
121B MSE 5.5 5.6 - - + +
122B ALA* 6.3 0.4 - - - -
125B ILE* 4.2 16.6 - - + -
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Residues in contact with THR 83 (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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79A THR* 2.9 35.9 + - - +
80A ASN* 2.6 29.6 + - - +
51B ALA* 5.5 3.1 - - - -
55B HIS* 4.0 16.8 - - + +
80B ASN 4.4 2.7 + - - -
82B VAL* 1.3 77.2 - - - +
84B PRO* 1.4 70.5 - - - +
86B ALA* 3.2 3.3 + - - +
87B ASN* 2.9 21.8 + - - +
418B LEU* 4.3 4.9 - - + +
420B SER* 3.8 18.6 - - - +
423B VAL* 4.3 3.8 - - + -
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Residues in contact with PRO 84 (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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51B ALA* 3.2 31.6 - - - +
54B GLY* 3.6 28.0 - - - -
55B HIS* 3.4 20.8 - - + +
58B GLU* 3.5 7.4 - - - +
80B ASN 4.0 6.3 - - - +
81B ALA* 3.1 16.2 - - - +
83B THR* 1.4 94.1 - - - +
85B ILE* 1.3 63.0 + - - +
87B ASN* 3.3 1.2 + - - +
88B ALA* 2.9 26.3 + - - +
97B PHE* 3.8 7.9 - - + -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 4.0 27.1 - - + -
81B ALA* 3.2 18.8 + - + +
82B VAL* 3.1 15.1 + - + +
84B PRO* 1.3 75.8 - - - +
86B ALA* 1.3 58.2 + - - +
88B ALA 3.4 0.2 + - - -
89B TRP* 3.0 27.0 + - - +
97B PHE* 3.7 30.7 - - + -
122B ALA* 4.7 5.8 - - + -
125B ILE* 3.5 29.4 - - + +
126B THR* 3.7 17.5 - - + -
156B PRO* 3.5 8.9 - - + +
158B LEU* 4.2 15.0 - - + -
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Residues in contact with ALA 86 (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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79A THR* 4.1 20.9 - - + -
116A ILE* 4.8 6.7 - - + -
82B VAL 2.9 13.0 + - - +
83B THR 3.6 6.7 - - - +
85B ILE* 1.3 74.5 - - - +
87B ASN* 1.3 66.1 + - - +
89B TRP* 3.2 8.0 + - - +
90B LEU* 3.0 27.5 + - - +
125B ILE* 3.8 23.8 - - + +
418B LEU* 4.4 11.9 - - + -
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Residues in contact with ASN 87 (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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55B HIS* 4.5 2.5 - - + -
58B GLU* 3.0 22.9 - - - +
62B ARG* 4.5 4.7 + - - -
83B THR 2.9 17.2 + - - +
84B PRO* 3.6 2.7 - - + +
86B ALA* 1.3 77.8 - - - +
88B ALA* 1.3 57.1 + - - +
90B LEU* 3.3 1.6 + - - +
91B ASP* 2.9 50.4 + - - +
415B HIS* 5.8 2.4 + - - +
416B GLY 4.8 6.5 - - - +
418B LEU* 3.3 34.7 - - + +
419B GLY 5.0 1.2 - - - +
420B SER* 5.0 1.8 - - - +
423B VAL* 3.7 28.5 - - - +
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Residues in contact with ALA 88 (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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58B GLU* 3.3 13.1 + - + +
84B PRO 2.9 17.1 + - - +
85B ILE 3.7 3.8 - - - +
87B ASN* 1.3 76.6 - - - +
89B TRP* 1.3 57.3 + - - +
92B ARG* 2.9 26.7 + - - -
93B THR* 3.1 40.8 + - + +
95B VAL* 4.6 1.8 - - + -
97B PHE* 4.6 4.5 - - + -
156B PRO* 3.6 16.5 - - + +
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Residues in contact with TRP 89 (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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115A GLY 4.4 8.1 + - - -
116A ILE* 4.4 3.1 - - + -
85B ILE 3.0 7.8 + - - +
86B ALA 3.3 9.6 - - - +
87B ASN 3.2 0.4 - - - -
88B ALA* 1.3 78.5 - - - +
90B LEU* 1.3 89.2 + - + +
91B ASP 3.3 0.3 + - - -
92B ARG* 3.5 11.1 + - - +
124B PRO 3.9 18.5 + - - -
125B ILE* 3.3 48.8 - - + +
126B THR* 3.6 26.2 - - - -
127B LYS* 3.9 15.0 - - + -
154B ARG 5.3 0.3 - - - +
155B GLY* 5.8 0.7 - - - -
156B PRO* 3.5 14.7 - - + +
279B ARG* 5.1 2.6 + - - -
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Residues in contact with LEU 90 (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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114A ALA 4.1 12.8 - - - +
115A GLY 4.2 8.7 - - - +
116A ILE* 3.7 26.0 - - + -
86B ALA 3.0 11.1 + - - +
87B ASN 3.9 3.8 - - - +
89B TRP* 1.3 103.7 - - + +
91B ASP* 1.3 61.1 + - - +
92B ARG 3.4 0.7 - - - -
279B ARG* 2.8 30.0 + - - +
417B TYR* 3.8 30.8 - - + -
418B LEU* 3.9 38.1 - - + +
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Residues in contact with ASP 91 (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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62B ARG* 3.9 19.7 + - - -
87B ASN* 2.9 35.6 + - - +
89B TRP 3.1 0.6 - - - -
90B LEU* 1.3 80.3 - - - +
92B ARG* 1.3 71.7 + - - +
93B THR* 3.1 21.0 - - + +
213B SER* 3.7 7.7 + - - -
217B ARG* 2.9 15.7 + - - +
240B GLU* 5.1 4.5 - - - +
279B ARG* 4.6 2.9 - - - +
416B GLY* 3.3 31.2 + - - -
417B TYR 3.8 2.6 + - - -
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Residues in contact with ARG 92 (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 ALA 2.9 5.8 + - - -
89B TRP 3.5 7.0 + - - +
90B LEU 3.4 2.0 - - - -
91B ASP* 1.3 78.0 - - - +
93B THR* 1.3 57.7 + - - +
153B PRO* 3.5 33.6 - - + +
154B ARG* 3.0 36.5 - - - +
213B SER* 3.5 16.2 + - - +
214B GLU* 3.9 20.8 - - - +
217B ARG* 2.9 19.4 + - - +
277B GLY 4.1 9.9 + - - -
279B ARG* 3.2 47.4 - - - +
302B ASP* 2.6 43.0 + - - -
303B PRO* 4.0 2.2 - - - +
304B ASP* 4.3 3.8 + - - +
307B GLU* 4.2 6.3 + - - +
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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