Contacts of the helix formed by residues 20 - 28 (chain A) in PDB entry 2AGA
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 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A CYS* 1.3 68.2 - - - +
21A GLN* 1.3 51.8 + - - +
22A HIS* 2.6 18.7 + - - -
23A CYS* 2.6 22.1 + - - +
24A LEU* 3.0 10.8 + - - +
79A PHE* 5.5 1.0 - - - +
80A PHE* 5.1 5.4 - - + +
85A ILE* 4.3 2.0 - - + -
124A HIS* 5.5 6.2 + - + +
125A TRP* 2.7 59.3 - - + +
127A THR* 4.9 2.2 - - - +
139A ASN* 5.4 7.4 - - - +
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Residues in contact with GLN 21 (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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16A GLY* 4.4 3.6 - - - +
18A LEU* 6.1 1.3 - - + -
19A CYS* 2.7 10.1 + - + +
20A ALA* 1.3 78.0 - - - +
22A HIS* 1.3 50.0 - - - +
24A LEU* 2.8 34.0 - - - +
25A ASN* 2.4 47.7 + - - +
33A PHE* 3.5 29.5 - - + +
34A SER 4.4 7.4 - - - +
35A PRO* 5.2 2.2 - - + -
38A LEU* 3.0 53.8 - - + +
80A PHE* 5.0 1.6 - - + -
85A ILE* 5.0 0.6 - - - +
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Residues in contact with HIS 22 (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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10A PHE* 5.6 8.9 - + - -
11A HIS* 5.8 0.2 - - + -
14A GLN* 3.3 31.6 - - + +
16A GLY 3.3 14.2 + - - +
17A SER* 3.3 20.0 + - - -
18A LEU 4.5 0.9 - - - +
19A CYS 2.8 12.7 + - - +
20A ALA 2.6 4.8 + - - -
21A GLN* 1.3 73.3 - - - +
23A CYS* 1.3 77.8 + - - +
25A ASN* 3.0 10.8 + - - +
26A ASN* 3.0 51.3 + - - +
138A LEU* 4.5 7.5 - - - +
139A ASN 4.5 11.6 + - - -
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Residues in contact with CYS 23 (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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20A ALA* 2.6 14.1 + - - +
22A HIS* 1.3 81.1 - - - +
24A LEU* 1.3 51.0 + - - +
26A ASN* 3.2 8.5 + - - +
27A LEU* 2.6 37.4 + - - +
127A THR* 2.8 27.4 - - - +
129A ARG* 5.5 0.5 + - - -
138A LEU* 2.9 56.5 - - + -
139A ASN* 3.3 14.6 - - - -
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Residues in contact with LEU 24 (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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20A ALA 3.0 8.4 + - - +
21A GLN* 2.8 40.8 - - - +
23A CYS* 1.3 78.4 - - - +
25A ASN* 1.3 51.2 - - - +
27A LEU* 3.5 13.5 - - + +
28A LEU* 2.6 46.9 + - + +
33A PHE* 4.0 13.0 - - + -
38A LEU* 4.6 1.1 - - + -
85A ILE* 3.4 38.4 - - + -
88A ALA* 4.2 10.5 - - + -
89A LEU* 3.4 32.3 - - + -
125A TRP* 6.1 0.2 - - - -
127A THR* 4.9 2.6 + - + +
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Residues in contact with ASN 25 (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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11A HIS* 3.5 2.4 - - - -
14A GLN* 3.0 30.7 + - - +
16A GLY* 3.5 7.6 - - - +
21A GLN* 2.4 56.7 + - - +
22A HIS* 3.0 5.2 + - - +
24A LEU* 1.3 75.9 - - - +
26A ASN* 1.3 54.8 + - - +
28A LEU* 4.6 0.6 - - - +
29A GLN 3.0 4.3 + - - -
30A GLY* 2.7 35.5 + - - -
31A GLU* 3.2 40.7 + - - +
33A PHE* 3.8 9.0 + - - +
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Residues in contact with ASN 26 (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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10A PHE* 5.3 5.1 - - - +
11A HIS* 2.7 35.4 - - + +
14A GLN* 2.4 31.4 - - - +
22A HIS* 3.0 40.7 + - - -
23A CYS* 3.5 9.3 - - - +
25A ASN* 1.3 73.8 - - - +
27A LEU* 1.3 63.2 + - - +
29A GLN* 2.9 18.5 + - - -
129A ARG* 4.6 12.4 - - - +
138A LEU* 4.1 15.9 - - + +
177A CYS* 3.9 15.6 - - - +
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Residues in contact with LEU 27 (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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23A CYS 2.6 21.5 + - - +
24A LEU* 3.5 27.6 - - + +
26A ASN* 1.3 71.1 - - - +
28A LEU* 1.3 63.9 + - + +
29A GLN* 2.9 10.0 + - - +
85A ILE* 5.0 2.0 - - + -
89A LEU* 4.5 11.7 - - + -
116A SER* 3.3 31.2 - - - +
118A ILE* 5.5 1.3 - - + -
127A THR* 4.7 16.8 - - + -
128A VAL 5.0 0.7 - - - +
129A ARG* 4.0 33.9 - - + +
170A VAL* 5.1 0.2 - - + -
174A LEU* 3.5 44.5 - - + +
175A PRO 3.9 2.9 - - - +
177A CYS* 5.2 0.7 - - - +
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Residues in contact with LEU 28 (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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24A LEU* 2.6 42.6 + - + +
25A ASN* 5.4 0.7 - - - -
27A LEU* 1.3 81.3 - - + +
29A GLN* 1.3 75.2 + - - +
30A GLY 2.9 12.7 + - - +
33A PHE* 4.4 6.3 - - + -
89A LEU* 3.8 21.8 - - + -
92A TRP* 3.0 69.9 - - + +
94A LEU* 4.7 4.5 - - + -
174A LEU* 4.8 0.7 - - + -
175A PRO* 3.1 23.6 - - + +
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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