Contacts of the strand formed by residues 41 - 50 (chain E) in PDB entry 1KQN
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 TYR 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E LYS* 3.7 13.0 + - - +
7E THR* 3.3 29.8 - - + +
9E VAL* 4.1 13.9 - - + -
35E MET* 3.8 43.0 + - + +
36E ASN* 3.8 18.1 - - - +
38E THR* 3.4 19.1 + - + -
40E ARG* 1.3 103.9 - - + +
42E THR* 1.3 66.9 + - - +
152E LYS* 4.6 17.2 + - - -
208E SER 4.9 2.3 + - - -
209E ASN* 5.2 1.7 + - - -
211E HIS* 3.4 32.5 + + - -
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Residues in contact with THR 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LYS* 3.4 23.8 + - - +
7E THR 2.9 12.0 + - - -
8E GLU* 3.2 15.3 - - + +
9E VAL* 2.9 22.7 + - - -
36E ASN* 3.4 6.7 - - - +
41E TYR* 1.3 77.4 + - - +
43E VAL* 1.3 65.6 + - - +
44E VAL* 3.4 16.9 + - + +
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Residues in contact with VAL 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.5 18.6 - - + +
11E LEU* 3.8 27.1 - - + -
32E LYS* 3.8 31.4 - - + +
35E MET* 3.5 29.8 - - + -
36E ASN* 2.7 27.7 + - - +
42E THR* 1.3 74.9 - - - +
44E VAL* 1.3 62.8 - - - +
45E LYS 4.3 2.5 - - - +
79E TRP* 3.9 18.6 - - + -
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Residues in contact with VAL 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E GLU* 3.7 28.9 - - + +
9E VAL 3.0 15.8 + - - +
10E VAL* 4.0 17.0 - - + -
42E THR* 3.6 21.3 - - + +
43E VAL* 1.3 76.3 - - - +
45E LYS* 1.3 69.7 + - + +
79E TRP* 4.5 13.7 - - - +
149E PRO* 4.4 11.7 - - + -
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Residues in contact with LYS 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL 3.8 1.1 + - - +
10E VAL* 3.4 12.8 - - + +
11E LEU 3.0 23.7 + - - -
43E VAL* 3.7 2.2 - - - +
44E VAL* 1.3 93.1 - - + +
46E GLY* 1.3 62.0 + - - +
47E ILE* 3.9 27.3 - - + +
79E TRP* 3.6 23.2 - - - +
81E GLU* 3.8 36.8 + - + +
105E LYS* 5.8 6.1 - - - +
106E LEU* 4.8 17.1 - - - +
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Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU* 3.5 6.1 - - - -
28E PHE* 3.6 11.9 - - - -
45E LYS* 1.3 73.7 - - - +
47E ILE* 1.3 64.7 + - - +
79E TRP* 3.1 30.6 + - - +
80E VAL* 3.3 3.5 - - - -
81E GLU* 2.9 28.2 + - - +
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Residues in contact with ILE 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL* 3.8 22.0 - - + -
11E LEU 2.8 11.3 + - - +
12E LEU* 3.4 23.4 - - + +
13E ALA 2.9 27.4 + - - -
28E PHE* 3.6 2.8 - - - -
45E LYS* 3.9 28.5 - - + +
46E GLY* 1.3 79.0 - - - +
48E ILE* 1.3 64.9 + - - +
49E SER 4.6 0.2 - - - +
81E GLU* 3.5 8.5 - - + +
82E VAL 5.0 0.2 - - - -
83E ASP* 3.6 31.9 - - + +
102E HIS* 3.8 24.9 - - + +
105E LYS* 6.1 0.7 - - - +
106E LEU* 6.2 2.0 - - + -
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Residues in contact with ILE 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ALA 3.8 3.6 - - - -
17E PHE* 4.0 25.1 - - + -
20E ILE* 3.9 24.2 - - + -
24E HIS* 6.1 0.4 - - + -
25E LEU* 4.7 4.3 - - + -
28E PHE* 3.5 28.0 - - + -
47E ILE* 1.3 71.4 - - - +
49E SER* 1.3 61.9 + - - +
50E PRO* 3.2 21.9 - - + +
70E ALA* 4.2 11.9 - - + +
74E THR* 3.9 14.6 - - + -
80E VAL* 3.8 19.5 - - + -
81E GLU 2.8 14.3 + - - +
82E VAL* 3.4 7.4 - - + -
83E ASP 2.9 24.0 + - - -
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Residues in contact with SER 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E LEU* 4.1 20.9 - - - -
13E ALA 3.1 12.2 + - - -
14E CYS* 3.6 5.5 - - - -
15E GLY 3.4 19.2 + - - -
17E PHE* 4.5 1.1 - - - -
47E ILE 3.7 0.4 + - - -
48E ILE* 1.3 74.0 - - - +
50E PRO* 1.3 63.8 + - - +
83E ASP* 3.8 14.9 + - - +
86E GLU* 2.6 45.3 + - - +
98E VAL* 4.0 4.0 - - - +
102E HIS* 4.9 2.4 + - - -
781E NAD 5.1 0.2 + - - -
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Residues in contact with PRO 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLY 3.4 8.1 - - - +
16E SER 4.8 0.2 - - - +
17E PHE* 4.1 9.4 - - + -
48E ILE* 3.2 25.4 - - + +
49E SER* 1.3 90.8 + - - +
51E VAL* 1.3 63.1 + - - +
52E GLY 3.9 0.3 + - - -
63E ALA 5.2 0.2 - - - +
66E ARG* 4.0 20.0 - - + +
67E VAL* 4.3 35.0 - - + +
70E ALA* 4.4 4.3 - - + -
82E VAL* 4.1 6.5 - - + -
83E ASP 3.7 10.6 - - - +
84E THR* 5.7 0.2 - - - -
86E GLU* 4.1 1.6 - - - -
87E SER* 3.8 19.5 + - - +
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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