Contacts of the strand formed by residues 29 - 35 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B LEU* 4.1 16.3 - - - +
22B VAL 3.3 5.4 - - - -
23B HIS* 3.5 35.1 - - + +
27B GLY 3.9 12.1 + - - +
28B ILE* 1.3 79.1 - - - +
30B GLY* 1.3 59.1 + - - +
94B ILE* 4.2 3.1 - - - -
97B LYS* 2.9 33.5 + - - +
381B GLU* 5.6 1.7 + - - -
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Residues in contact with GLY 30 (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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20B VAL 3.6 1.0 - - - +
21B LEU* 3.3 9.6 - - - +
22B VAL 3.0 32.3 + - - -
29B THR* 1.3 75.3 - - - +
31B LEU* 1.3 60.1 + - - -
90B ALA* 3.5 27.6 - - - +
93B ASP* 3.5 7.6 - - - -
94B ILE* 3.7 7.7 - - - +
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Residues in contact with LEU 31 (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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19B TRP* 4.2 10.3 - - + -
20B VAL 3.5 7.6 - - - +
21B LEU* 3.9 18.4 - - + -
30B GLY* 1.3 72.4 - - - -
32B GLY* 1.3 80.1 - - - +
89B ILE* 3.5 12.0 - - - +
90B ALA* 3.5 6.2 - - - -
93B ASP* 2.8 18.6 + - - +
97B LYS* 6.0 0.2 - - - +
326B VAL* 3.6 23.7 - - + +
378B LEU* 3.4 20.0 - - + +
380B LEU* 3.8 13.7 - - + +
381B GLU* 4.0 4.3 - - - -
382B LEU* 3.6 46.0 - - + +
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Residues in contact with GLY 32 (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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19B TRP* 3.5 3.1 - - - -
20B VAL 2.7 36.4 + - - -
31B LEU* 1.3 84.9 - - - +
33B GLU* 1.3 62.2 + - - +
86B ALA* 3.3 24.7 - - - -
89B ILE* 4.1 4.0 - - - -
90B ALA* 3.5 6.3 - - - +
326B VAL* 4.2 2.5 - - - -
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Residues in contact with GLU 33 (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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17B LEU* 3.7 10.5 - - + +
18B LEU 3.2 14.1 - - - +
19B TRP* 2.9 26.2 + - + -
32B GLY* 1.3 74.8 - - - +
34B THR* 1.3 68.1 + - - +
35B PHE* 6.2 0.2 - - - +
86B ALA* 3.5 19.1 - - - +
89B ILE* 3.7 8.5 - - + +
295B SER* 3.6 12.1 - - - -
324B GLY* 3.2 22.5 + - - +
325B PRO* 3.3 10.7 - - - +
326B VAL* 3.2 32.7 + - + +
327B VAL* 2.9 32.2 + - + +
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Residues in contact with THR 34 (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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16B ASN 3.9 0.2 - - - +
17B LEU* 3.8 4.0 - - - +
18B LEU* 2.9 59.6 + - + +
33B GLU* 1.3 80.0 - - - +
35B PHE* 1.3 67.6 + - - +
36B TYR 5.2 2.5 - - - +
38B ALA* 6.0 0.2 - - - -
41B ALA* 4.3 5.2 - - + -
82B ARG* 3.4 43.3 - - + +
86B ALA* 4.1 3.6 - - + -
295B SER* 3.1 28.6 + - - -
327B VAL* 5.0 1.3 - - - -
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Residues in contact with PHE 35 (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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14B PHE* 5.7 2.5 - - + -
16B ASN* 3.5 22.0 - - + -
17B LEU* 3.9 35.4 - - + -
33B GLU* 6.2 0.2 - - - +
34B THR* 1.3 80.3 + - - +
36B TYR* 1.3 116.0 + + - +
82B ARG* 3.4 6.6 - - - -
125B HIS* 6.1 4.7 - + - -
295B SER* 4.2 2.8 + - - +
296B TRP* 3.0 26.6 + - - +
322B CYS 5.1 2.9 - - - -
323B THR* 3.6 48.2 - - + +
324B GLY 4.1 3.8 - - - +
327B VAL* 6.1 0.9 - - + -
350B PHE* 6.0 2.2 - + - -
354B TRP* 5.0 11.0 - + - -
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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