Contacts of the strand formed by residues 29 - 35 (chain A) in PDB entry 2POD
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 THR 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.5 4.9 - - - -
22A VAL 3.3 5.2 - - - -
23A HIS* 3.3 34.3 - - + +
27A GLY* 3.6 13.0 + - - +
28A ILE* 1.3 77.9 - - - +
30A GLY* 1.3 60.1 + - - +
94A ILE* 4.2 2.5 - - - -
97A LYS* 2.7 41.6 + - - +
381A GLU* 5.5 5.5 + - - +
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Residues in contact with GLY 30 (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 VAL 3.6 0.5 - - - +
21A LEU* 3.3 11.7 - - - +
22A VAL 2.9 31.7 + - - -
29A THR* 1.3 73.4 - - - +
31A LEU* 1.3 61.5 + - - -
90A ALA* 3.5 26.5 - - - +
93A ASP* 3.4 7.0 - - - -
94A ILE* 3.6 11.1 - - - +
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Residues in contact with LEU 31 (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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19A TRP* 4.1 11.2 - - + -
20A VAL 3.5 7.9 - - - +
21A LEU* 3.8 16.4 - - + -
30A GLY* 1.3 71.4 - - - -
32A GLY* 1.3 80.2 + - - +
89A ILE* 3.6 6.4 - - - +
90A ALA* 3.5 10.6 - - - -
93A ASP* 2.9 17.1 + - - +
97A LYS* 5.8 0.4 - - - +
326A VAL* 3.8 12.5 - - + +
378A LEU* 3.4 21.3 - - + +
380A LEU* 3.7 26.9 - - + +
381A GLU* 3.9 4.7 - - + -
382A LEU* 3.5 45.5 - - + +
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Residues in contact with GLY 32 (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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19A TRP* 3.4 4.9 - - - -
20A VAL* 2.8 34.6 + - - +
31A LEU* 1.3 81.6 - - - +
33A GLU* 1.3 63.5 + - - +
86A ALA* 3.3 23.3 - - - -
89A ILE* 4.1 4.5 - - - -
90A ALA* 3.5 8.2 - - - +
326A VAL* 4.4 1.6 - - - -
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Residues in contact with GLU 33 (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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17A LEU* 3.7 10.4 - - + +
18A LEU 3.2 13.7 - - - +
19A TRP* 3.0 25.3 + - + -
32A GLY* 1.3 75.9 - - - +
34A THR* 1.3 65.1 + - - +
86A ALA* 3.6 12.4 - - - +
89A ILE* 3.5 14.4 - - - +
295A SER* 3.4 17.0 - - - -
324A GLY* 3.2 22.5 + - - -
325A PRO* 3.4 10.7 - - - +
326A VAL* 3.2 31.9 + - + +
327A VAL* 2.9 31.8 + - + +
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Residues in contact with THR 34 (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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17A LEU* 3.7 9.2 - - - +
18A LEU* 3.0 59.0 + - + +
33A GLU* 1.3 75.2 - - - +
35A PHE* 1.3 75.2 + - - +
36A TYR 5.3 0.9 - - - +
38A ALA* 6.2 0.2 - - - -
41A ALA* 4.4 4.9 - - + -
82A ARG* 3.5 40.9 - - + +
86A ALA* 3.9 3.3 - - + +
295A SER* 3.0 29.1 + - - -
296A TRP* 3.8 0.7 - - - -
327A VAL* 4.9 1.6 - - - -
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Residues in contact with PHE 35 (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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14A PHE* 6.0 2.5 - - + -
16A ASN* 3.4 31.4 - - + -
17A LEU* 4.0 22.9 - - + -
34A THR* 1.3 81.9 + - - +
36A TYR* 1.3 118.5 - + - +
82A ARG* 3.5 6.1 - - - -
125A HIS* 5.7 10.5 - + - -
295A SER* 4.1 3.4 + - - +
296A TRP* 3.0 23.9 + - - +
322A CYS 5.0 4.7 - - - -
323A THR* 3.7 49.1 - - + -
324A GLY 4.1 3.1 - - - +
327A VAL* 6.1 0.2 - - + -
350A PHE* 6.0 2.0 - + - -
354A TRP* 5.0 10.8 - + - -
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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