Contacts of the strand formed by residues 7 - 15 (chain E) in PDB entry 1KR2
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 7 (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* 1.3 71.6 - - - +
8E GLU* 1.3 76.9 + - - +
9E VAL* 4.5 2.7 - - + -
40E ARG 3.0 9.0 + - - -
41E TYR* 3.3 30.5 - - + +
42E THR* 2.9 23.0 + - - -
149E PRO* 5.9 0.2 - - + -
150E LYS* 4.4 23.3 - - + -
152E LYS* 6.2 0.4 - - - -
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Residues in contact with GLU 8 (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 3.7 5.6 + - - +
7E THR* 1.3 83.3 - - - +
9E VAL* 1.3 59.7 + - - +
42E THR* 3.1 16.5 - - - +
44E VAL* 3.5 25.5 - - + +
147E ALA 4.4 9.3 - - - +
148E VAL 5.6 0.2 - - - -
149E PRO* 3.5 30.2 - - + +
150E LYS 3.0 22.0 + - - -
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Residues in contact with VAL 9 (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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7E THR* 3.8 4.7 - - + +
8E GLU* 1.3 81.0 - - - +
10E VAL* 1.3 66.5 + - - +
11E LEU* 3.6 23.3 - - + -
35E MET* 4.4 8.1 - - + -
41E TYR* 3.5 36.6 - - + -
42E THR 2.7 12.2 + - - +
43E VAL* 3.4 12.8 - - + +
44E VAL* 2.8 29.7 + - - +
45E LYS 3.7 0.9 + - - -
150E LYS* 3.3 12.3 - - + +
152E LYS* 3.5 25.8 - - + -
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Residues in contact with VAL 10 (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* 1.3 81.1 - - - +
11E LEU* 1.3 62.3 + - - +
12E LEU 3.8 0.2 + - - -
44E VAL* 3.7 18.4 - - + -
45E LYS* 3.3 20.9 - - + +
47E ILE* 4.1 28.3 - - + -
106E LEU* 4.0 34.1 - - + -
149E PRO* 4.1 8.1 - - + -
150E LYS 2.8 12.0 + - - +
151E VAL* 3.2 10.7 - - + +
152E LYS 2.8 31.4 + - - +
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Residues in contact with LEU 11 (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* 3.6 17.9 - - + -
10E VAL* 1.3 72.3 - - - +
12E LEU* 1.3 54.4 + - - +
28E PHE* 3.8 13.4 - - + +
31E ALA* 3.8 26.0 - - + -
32E LYS 4.1 8.1 - - - +
35E MET* 4.8 2.5 - - + -
43E VAL* 3.9 24.9 - - + -
45E LYS 3.0 7.2 + - - +
46E GLY* 3.3 0.9 - - - -
47E ILE* 2.7 33.8 + - - +
79E TRP* 4.1 13.0 - - + -
152E LYS* 3.6 5.6 - - + +
154E LEU* 4.3 13.7 - - + -
184E ILE* 3.2 33.9 - - + -
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Residues in contact with LEU 12 (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 0.4 + - + -
11E LEU* 1.3 72.8 - - - +
13E ALA* 1.3 61.0 + - - +
14E CYS* 4.1 9.2 - - - -
47E ILE* 3.4 35.7 - - + +
49E SER* 4.0 17.3 - - - -
98E VAL* 3.8 22.7 - - + -
99E LEU* 3.6 32.8 - - + -
102E HIS* 4.1 16.4 - - + -
151E VAL* 3.9 19.3 - - + -
152E LYS 3.0 7.7 + - - +
153E LEU* 3.3 9.8 - - + +
154E LEU* 2.8 25.4 + - - +
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Residues in contact with ALA 13 (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 4.1 0.4 - - - -
12E LEU* 1.3 73.6 - - - +
14E CYS* 1.3 62.8 + - - +
17E PHE* 3.7 18.6 - - + -
27E LEU* 6.3 2.2 - - + -
28E PHE* 3.5 31.0 - - + -
47E ILE 2.8 8.9 + - - +
48E ILE* 4.8 0.4 - - - -
49E SER* 3.0 26.2 + - - -
154E LEU* 3.7 20.0 - - + +
813E TAD 5.7 3.4 - - - -
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Residues in contact with CYS 14 (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* 4.0 14.6 + - - -
13E ALA* 1.3 77.2 - - - +
15E GLY* 1.3 57.9 + - - +
17E PHE* 3.6 2.4 - - - -
49E SER* 3.6 7.6 - - - +
86E GLU* 3.8 11.2 - - - +
95E THR* 4.3 23.8 - - + +
98E VAL* 3.7 35.9 - - - -
153E LEU* 4.3 11.1 - - + +
154E LEU 4.5 0.6 + - - +
159E LEU* 4.6 5.5 - - + +
813E TAD 3.7 38.2 + - - +
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Residues in contact with GLY 15 (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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14E CYS* 1.3 74.8 - - - +
16E SER* 1.3 59.7 + - - -
17E PHE* 3.0 21.3 - - - -
49E SER 3.6 2.6 + - - -
51E VAL* 2.9 22.7 + - - -
86E GLU* 5.4 0.2 + - - -
813E TAD 3.0 39.1 + - - -
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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