Contacts of the strand formed by residues 32 - 40 (chain A) in PDB entry 2CP2
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 PRO 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.3 48.0 + - + +
25A VAL 3.1 10.1 - - - +
26A TRP* 3.4 46.2 - - + +
31A LYS* 1.3 95.3 - - + +
33A GLY* 1.3 58.4 + - - +
53A LEU* 4.0 9.9 - - - +
54A ASP* 4.5 5.4 + - - +
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Residues in contact with GLY 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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23A GLU 3.0 6.0 - - - +
24A ARG* 4.2 4.3 - - - -
25A VAL* 2.6 32.0 + - - +
27A VAL* 5.3 0.4 - - - -
31A LYS 3.7 0.4 + - - -
32A PRO* 1.3 75.8 - - - +
34A VAL* 1.3 63.7 + - - -
35A VAL 3.5 0.7 + - - -
51A VAL* 3.3 19.5 - - - +
52A VAL 3.2 13.2 - - - -
53A LEU* 4.6 4.5 - - - -
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Residues in contact with VAL 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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22A GLY* 4.3 14.8 - - - -
23A GLU 3.3 8.5 - - - +
24A ARG* 4.2 20.9 - - + +
33A GLY* 1.3 72.5 - - - -
35A VAL* 1.3 70.3 + - - +
36A GLN* 4.5 9.1 - - + +
51A VAL* 3.9 0.2 - - - -
52A VAL* 2.6 53.3 + - + +
53A LEU 6.1 1.3 - - - -
54A ASP* 5.3 5.8 - - - +
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Residues in contact with VAL 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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19A PHE* 4.9 2.0 - - + -
20A VAL 3.7 9.0 - - - +
21A VAL* 3.5 2.6 - - - +
22A GLY* 2.9 28.1 + - - -
23A GLU* 3.2 23.2 + - + +
25A VAL* 3.5 32.1 - - + -
34A VAL* 1.3 72.4 - - - +
36A GLN* 1.3 62.8 + - - +
37A TYR 3.7 0.7 - - - +
38A LEU* 3.4 43.3 - - + -
49A ALA* 5.1 0.2 - - + -
50A GLY 3.1 19.3 - - - +
51A VAL* 4.1 8.1 - - + +
85A LEU* 4.6 3.8 - - + -
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Residues in contact with GLN 36 (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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21A VAL* 3.1 32.7 - - - +
22A GLY* 4.9 3.8 - - - +
34A VAL* 3.5 11.2 + - + +
35A VAL* 1.3 81.1 + - - +
37A TYR* 1.3 67.6 + - - +
50A GLY 3.2 4.4 + - - -
52A VAL* 3.9 20.4 - - + -
70A PHE* 3.7 33.0 - - + +
71A GLU 5.3 3.6 + - - +
72A CYS* 4.9 6.3 - - - -
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Residues in contact with TYR 37 (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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36A GLN* 1.3 84.9 - - - +
38A LEU* 1.3 80.2 + - - +
39A GLY* 5.3 1.6 - - - -
40A GLU 4.8 12.3 - - - -
41A THR* 5.7 1.8 - - + -
50A GLY* 2.6 40.8 + - - +
69A TYR* 3.6 57.2 - + + -
70A PHE* 3.9 18.6 - + + -
79A PHE* 4.5 4.5 - + + -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.5 14.1 - - + -
17A GLY 5.3 0.9 - - - +
19A PHE* 2.8 41.7 - - + +
20A VAL* 3.6 3.6 - - - -
21A VAL* 3.6 28.8 - - + +
35A VAL* 3.4 23.6 - - + -
36A GLN 4.4 0.2 + - - -
37A TYR* 1.3 86.9 - - - +
39A GLY* 1.3 57.7 + - - +
48A TRP 4.0 2.5 - - - -
49A ALA* 3.6 26.9 - - + -
82A PRO* 5.6 0.2 - - + -
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Residues in contact with GLY 39 (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 LEU* 3.9 20.7 - - - +
37A TYR* 5.3 3.1 - - - -
38A LEU* 1.3 75.2 - - - +
40A GLU* 1.3 63.7 + - - -
41A THR* 5.8 0.2 - - - -
47A GLN* 4.1 2.9 - - - -
48A TRP* 2.5 48.9 + - - +
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Residues in contact with GLU 40 (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 LEU* 5.6 2.0 - - - -
37A TYR* 4.8 12.2 - - - -
39A GLY* 1.3 75.6 - - - -
41A THR* 1.3 67.9 + - - +
42A GLN* 5.3 1.7 - - - +
44A ALA 5.9 0.2 - - - +
45A PRO* 6.0 0.9 - - + -
46A GLY 3.9 14.1 - - - +
47A GLN* 3.2 25.4 + - - +
69A TYR* 5.1 0.3 - - - -
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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