Contacts of the strand formed by residues 12 - 17 (chain D) in PDB entry 4CQM
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 12 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 3.3 34.6 + - + +
10D ARG 3.2 2.2 - - - +
11D SER* 1.3 79.1 - - - +
13D LEU* 1.3 59.8 + - - +
35D GLY 4.7 0.6 + - - -
36D ALA* 3.4 7.5 - - + +
37D THR* 3.0 26.5 + - - +
95D ARG* 4.1 3.6 - - - +
98D SER* 3.9 13.7 - - - +
99D VAL* 5.0 7.2 - - + -
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 1.3 71.3 - - - +
14D ALA* 1.3 60.0 + - - +
37D THR* 3.3 21.1 - - + +
39D ALA* 4.5 8.3 - - + -
89D VAL* 3.7 17.0 - - + -
93D PHE* 3.6 49.1 - - + -
95D ARG* 3.4 47.5 - - + +
96D PRO 4.5 2.7 - - - +
97D PRO* 3.4 17.1 - - + +
98D SER* 3.0 28.4 + - - +
99D VAL* 3.2 6.7 + - - -
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Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 6.2 0.4 - - + -
12D ALA 3.8 0.8 + - - -
13D LEU* 1.3 72.3 - - - +
15D LEU* 1.3 56.7 + - - +
16D VAL* 3.8 1.5 + - + -
31D LEU* 3.6 33.2 - - + -
36D ALA* 4.8 7.4 - - + -
37D THR 2.9 13.5 + - - +
38D VAL* 3.3 10.9 - - + +
39D ALA* 2.6 33.5 + - - +
97D PRO* 4.9 0.2 - - - -
99D VAL* 3.2 19.1 - - + -
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU 4.0 1.4 + - - -
14D ALA* 1.3 71.9 - - - +
16D VAL* 1.3 59.3 + - - +
17D THR* 4.8 2.2 - - + -
39D ALA* 3.3 28.3 - - + +
41D CYS* 4.3 19.1 - - + -
72D PHE* 5.2 0.4 - - + -
85D LEU* 4.1 16.2 - - + -
86D LEU* 3.8 37.9 - - + -
89D VAL* 4.0 12.3 - - + -
97D PRO* 3.7 21.5 - - + +
99D VAL 2.7 10.0 + - - +
100D VAL* 3.5 15.3 - - + +
101D VAL* 2.7 32.7 + - - +
134D VAL* 4.8 4.0 - - + -
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Residues in contact with VAL 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ALA 4.4 2.0 - - - +
15D LEU* 1.3 76.8 - - - +
17D THR* 1.3 71.3 + - - +
19D ALA* 3.3 6.8 - - + +
24D GLY* 3.4 29.4 - - - +
27D VAL* 3.9 25.4 - - + -
28D SER* 3.7 14.6 - - - +
31D LEU* 4.1 13.5 - - + -
38D VAL* 4.2 10.1 - - + -
39D ALA 2.9 10.5 + - - +
41D CYS* 2.8 30.8 + - - +
101D VAL* 3.4 15.5 - - + +
103D CYS* 4.4 2.0 - - - -
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Residues in contact with THR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 4.8 5.4 - - + -
16D VAL* 1.3 73.3 - - - +
18D GLY* 1.3 67.0 + - - +
19D ALA 3.1 3.0 + - - -
41D CYS* 3.3 8.5 - - + -
76D VAL* 4.2 11.4 - - + +
85D LEU* 4.2 17.0 - - + -
101D VAL 2.9 9.4 + - - +
102D SER* 3.3 9.0 - - - -
103D CYS* 3.2 34.7 + - - +
104D ALA* 3.3 17.3 + - - +
134D VAL* 4.2 32.0 - - + +
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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