Contacts of the strand formed by residues 26 - 33 (chain B) in PDB entry 2G1Y
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 GLN 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B GLY* 3.5 3.0 - - - -
21B ILE 2.9 33.1 + - - +
24B PRO* 4.1 7.4 - - + +
25B PRO* 1.3 73.9 - - - +
27B THR* 1.3 59.7 + - - +
28B PHE* 3.1 21.4 - - + -
57B LYS* 4.4 11.2 - - - +
58B LEU 3.2 25.1 + - - -
59B PHE* 3.6 14.8 - - - +
60B ASP* 3.0 40.3 + - - +
63B ASP* 4.2 11.9 - - + +
64B SER* 5.2 1.9 - - - -
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Residues in contact with THR 27 (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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18B GLU* 3.8 33.0 - - + +
19B ILE 3.6 6.7 - - - +
20B GLY* 4.7 1.7 - - - -
25B PRO* 4.0 5.1 + - - +
26B GLN* 1.3 70.9 - - - +
28B PHE* 1.3 64.6 + - - +
29B LYS* 6.1 0.9 - - + -
57B LYS* 3.0 40.1 + - - +
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Residues in contact with PHE 28 (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 GLY 3.4 1.0 - - - +
18B GLU* 3.2 6.7 - - - -
19B ILE* 3.1 32.7 + - + +
21B ILE* 3.7 34.1 - - + -
26B GLN* 3.1 41.7 - - + -
27B THR* 1.3 77.7 - - - +
29B LYS* 1.3 62.3 + - - +
30B VAL* 3.6 15.7 + - + +
41B VAL* 4.1 15.5 - - + -
57B LYS* 4.0 26.7 - - + -
58B LEU 3.6 25.8 - - - -
59B PHE* 3.6 26.9 - + + -
120B ASP* 3.6 11.2 - - + +
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Residues in contact with LYS 29 (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 TYR* 4.1 25.3 - - + -
17B GLY 3.3 6.3 - - - +
18B GLU* 4.9 11.9 - - + -
27B THR* 6.1 1.1 - - + -
28B PHE* 1.3 72.1 - - - +
30B VAL* 1.3 58.8 + - - +
118B GLU* 3.8 16.5 + - - +
119B PHE* 3.5 8.2 - - - +
120B ASP* 2.5 52.6 + - - +
121B GLY 3.1 5.9 + - - -
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Residues in contact with VAL 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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16B TYR* 3.0 6.7 - - - +
17B GLY 2.7 37.1 + - - +
19B ILE* 3.6 42.6 - - + -
28B PHE* 4.2 9.4 - - + +
29B LYS* 1.3 79.3 - - - +
31B VAL* 1.3 61.5 + - - +
32B PHE* 3.8 14.6 + - + -
39B VAL* 6.3 0.2 - - + -
41B VAL* 4.6 4.7 - - + -
121B GLY* 3.2 24.9 - - - +
122B VAL 4.3 0.2 - - - +
123B VAL* 3.4 28.7 - - + -
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Residues in contact with VAL 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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15B TYR 3.3 18.6 - - - +
16B TYR* 4.1 0.4 - - + -
30B VAL* 1.3 74.9 - - - +
32B PHE* 1.3 71.7 + - - +
33B ASP 3.3 3.1 + - - -
119B PHE* 3.5 42.4 - - + -
121B GLY 3.2 6.8 + - - +
122B VAL* 3.6 2.8 - - - +
123B VAL 3.0 23.2 + - - -
157B TYR* 4.8 0.4 - - - +
223B GLY* 4.2 2.7 - - - -
886B 5IG 3.5 58.6 - - + +
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Residues in contact with PHE 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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5B VAL* 4.0 24.0 - - + -
7B LEU* 3.9 31.2 - - + -
15B TYR 4.6 1.4 + - - -
17B GLY* 4.1 2.9 - - - -
19B ILE* 3.7 27.4 - - + -
30B VAL* 3.8 17.3 - - + -
31B VAL* 1.3 75.7 - - - +
33B ASP* 1.3 52.8 + - - +
94B VAL* 4.3 13.7 - - + -
123B VAL* 3.6 30.7 - - + -
125B MET* 4.4 8.3 - - + -
155B PHE* 3.1 31.5 - - + -
157B TYR* 3.9 5.0 + - - -
171B ILE* 3.7 21.3 - - + -
173B LEU* 5.9 1.6 - - + -
222B THR* 2.7 23.0 + - - -
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Residues in contact with ASP 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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31B VAL 3.3 0.6 + - - -
32B PHE* 1.3 70.9 - - - +
34B THR* 1.3 55.7 + - - +
35B GLY 2.6 24.1 + - - -
36B SER* 2.6 33.8 + - - +
122B VAL* 3.6 16.8 - - + -
123B VAL 3.0 8.4 + - - +
124B GLY* 3.5 0.2 - - - -
125B MET* 2.6 29.0 + - - -
221B ASP* 2.9 15.9 - - - +
222B THR* 3.5 1.3 - - - -
223B GLY* 3.3 3.8 - - - +
886B 5IG 2.3 46.2 + - + +
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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