Contacts of the helix formed by residues 81 - 92 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU* 4.2 6.3 - - + +
54A GLY* 5.7 0.7 - - - -
72A VAL* 4.2 21.5 - - + -
77A GLY 3.5 11.2 + - - +
78A PHE* 2.9 13.9 + - + +
80A ASN* 1.3 78.5 - - - +
82A VAL* 1.3 62.9 + - - +
83A THR 3.3 1.8 - - - -
84A PRO* 3.0 19.2 - - + +
85A ILE* 3.2 19.9 + - + +
97A PHE* 4.5 17.7 - - + -
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.8 36.6 - - + +
79A THR* 3.2 20.7 + - - +
80A ASN 3.3 0.2 - - - -
81A ALA* 1.3 78.3 - - - +
83A THR* 1.3 58.2 + - - +
85A ILE* 3.1 9.7 + - + +
86A ALA* 2.9 25.8 + - - +
121A MSE 5.4 6.3 - - + +
122A ALA* 6.2 0.2 - - - -
125A ILE* 4.1 15.8 - - + +
79B THR* 4.2 21.8 - - + +
82B VAL* 4.5 21.5 - - + -
121B MSE 4.7 6.7 - - + -
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Residues in contact with THR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 5.4 2.9 - - - -
55A HIS* 4.0 15.7 - - + +
79A THR 5.0 0.2 + - - -
80A ASN 4.4 3.6 + - - -
82A VAL* 1.3 77.4 - - - +
84A PRO* 1.4 69.2 - - - +
86A ALA* 3.2 3.7 + - - +
87A ASN* 3.0 21.7 + - - +
418A LEU* 4.2 4.4 - - + +
420A SER* 3.9 17.7 - - - +
423A VAL* 4.3 4.5 - - + -
79B THR* 2.8 36.2 + - - +
80B ASN* 2.7 28.7 + - - +
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Residues in contact with PRO 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 3.2 32.3 - - - +
54A GLY* 3.6 28.0 - - - -
55A HIS* 3.4 21.1 - - + +
58A GLU* 3.4 7.5 - - - +
80A ASN 4.1 6.3 - - - +
81A ALA* 3.0 19.7 - - - +
83A THR* 1.4 86.7 - - - +
85A ILE* 1.3 66.8 + - - +
87A ASN 3.3 0.2 + - - -
88A ALA* 3.0 26.2 + - - +
97A PHE* 3.8 7.6 - - + -
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 4.0 28.5 - - + -
81A ALA* 3.2 17.2 + - + +
82A VAL* 3.1 13.5 + - + +
84A PRO* 1.3 76.5 - - - +
86A ALA* 1.3 57.4 + - - +
88A ALA 3.4 0.2 + - - -
89A TRP* 2.9 27.5 + - - +
97A PHE* 3.7 31.9 - - + -
122A ALA* 4.6 6.3 - - + -
125A ILE* 3.5 30.7 - - + +
126A THR* 3.7 15.7 - - + -
156A PRO* 3.5 7.7 - - + +
158A LEU* 4.2 15.9 - - + -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL 2.9 14.9 + - - +
83A THR 3.7 4.0 - - - +
85A ILE* 1.3 77.7 - - - +
87A ASN* 1.3 62.6 + - - +
89A TRP* 3.2 8.2 + - - +
90A LEU* 3.1 26.0 + - - +
125A ILE* 3.9 24.9 - - + +
418A LEU* 4.4 11.7 - - + -
79B THR* 4.2 20.6 - - + -
116B ILE* 4.7 8.1 - - + -
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A HIS* 4.5 2.9 - - + -
58A GLU* 3.1 22.5 - - - +
62A ARG* 4.6 3.8 + - - -
83A THR 3.0 15.4 + - - +
84A PRO* 3.7 2.5 - - + +
86A ALA* 1.3 78.9 - - - +
88A ALA* 1.3 57.0 + - - +
90A LEU* 3.4 1.2 + - - +
91A ASP* 2.8 49.5 + - - +
415A HIS* 5.8 2.4 + - - +
416A GLY 4.8 6.1 + - - +
418A LEU* 3.2 36.1 - - + +
419A GLY 4.8 1.2 - - - +
420A SER* 5.0 2.2 - - - +
423A VAL* 3.6 29.0 - - - +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU* 3.3 20.7 + - + +
84A PRO 3.0 17.3 + - - +
85A ILE 3.7 3.6 - - - +
87A ASN* 1.3 75.3 - - - +
89A TRP* 1.3 58.5 + - - +
92A ARG* 2.9 27.0 + - - -
93A THR* 3.1 33.6 + - + +
95A VAL* 4.6 2.0 - - + -
97A PHE* 4.6 4.9 - - + -
156A PRO* 3.7 16.7 - - + +
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Residues in contact with TRP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ILE 2.9 8.3 + - - +
86A ALA 3.2 9.4 + - - +
88A ALA* 1.3 78.2 - - - +
90A LEU* 1.3 90.7 + - + +
92A ARG* 3.5 13.0 + - - +
124A PRO 3.9 14.4 + - - -
125A ILE* 3.2 53.4 - - + +
126A THR* 3.6 25.8 - - - -
127A LYS* 3.9 14.4 - - + -
154A ARG 5.4 0.2 - - - +
155A GLY* 5.7 0.4 - - - -
156A PRO* 3.5 15.4 - - + +
279A ARG* 5.1 1.2 + - - -
115B GLY 4.6 8.1 + - - -
116B ILE* 4.5 2.5 - - + -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA 3.1 11.7 + - - +
87A ASN 4.0 3.1 - - - +
89A TRP* 1.3 100.7 - - + +
91A ASP* 1.3 57.4 + - - +
279A ARG* 2.7 35.4 + - - +
417A TYR* 3.8 30.2 - - + -
418A LEU* 3.9 37.7 - - + +
114B ALA 4.2 12.3 - - - +
115B GLY* 4.5 7.2 - - - +
116B ILE* 3.7 26.2 - - + -
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU* 4.5 0.2 - - - +
62A ARG* 4.0 20.0 + - - -
87A ASN* 2.8 36.0 + - - +
89A TRP 3.2 0.4 - - - -
90A LEU* 1.3 80.1 - - - +
92A ARG* 1.3 70.7 + - - +
93A THR* 3.1 22.2 - - + +
213A SER* 3.7 8.5 + - - -
217A ARG* 3.1 15.0 + - - +
240A GLU* 5.2 4.0 - - - +
279A ARG* 4.5 2.7 - - - +
416A GLY* 3.2 33.1 + - - -
417A TYR 3.8 2.6 + - - -
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA 2.9 6.8 + - - -
89A TRP 3.5 7.0 + - - +
90A LEU 3.4 2.8 - - - -
91A ASP* 1.3 78.0 - - - +
93A THR* 1.3 56.6 + - - +
153A PRO* 3.5 35.3 - - + +
154A ARG* 3.0 34.7 - - - +
213A SER* 3.7 14.8 + - - +
214A GLU* 3.9 22.4 - - - +
217A ARG* 2.8 21.7 + - - +
277A GLY 4.1 8.7 + - - -
279A ARG* 3.3 49.1 - - - +
302A ASP* 2.6 43.2 + - - -
303A PRO* 3.9 1.8 - - - +
304A ASP* 4.2 4.0 + - - +
307A GLU* 4.1 6.9 - - - +
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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