Contacts of the strand formed by residues 150 - 156 (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 LYS 150 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E THR* 4.4 20.0 - - + -
8E GLU 3.0 12.0 + - - +
9E VAL* 3.3 9.3 - - + +
10E VAL* 2.8 28.8 + - - -
103E GLN* 3.4 6.7 - - - +
148E VAL 4.2 7.4 - - - +
149E PRO* 1.3 75.6 - - - +
151E VAL* 1.3 60.3 + - - +
152E LYS* 4.4 22.4 - - - +
180E ASN 5.8 3.6 - - - +
181E TYR 5.6 0.9 - - - +
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Residues in contact with VAL 151 (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* 3.2 13.2 - - + +
12E LEU* 3.9 21.5 - - + -
99E LEU* 3.6 28.5 - - + +
102E HIS* 4.0 7.4 - - + -
103E GLN* 3.0 35.1 + - + +
106E LEU* 3.3 31.2 - - + -
150E LYS* 1.3 74.2 - - - +
152E LYS* 1.3 61.9 + - - +
181E TYR* 3.6 29.8 - - + +
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Residues in contact with LYS 152 (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* 6.2 0.7 - - - -
9E VAL* 3.5 32.3 - - + -
10E VAL 2.8 9.0 + - - +
11E LEU* 3.6 3.7 - - + +
12E LEU* 3.0 24.1 + - - -
35E MET* 5.0 5.2 - - + -
41E TYR* 4.8 15.2 + - - -
99E LEU* 4.3 4.0 - - - -
150E LYS* 3.9 23.5 - - + +
151E VAL* 1.3 78.8 - - - +
153E LEU* 1.3 62.7 + - - +
154E LEU 3.4 0.3 + - - -
181E TYR 2.7 25.7 + - - +
182E GLY* 3.8 9.4 - - - +
184E ILE* 4.2 22.0 - - + -
209E ASN* 2.9 32.5 + - - +
211E HIS* 5.5 3.5 + - + -
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Residues in contact with LEU 153 (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 3.3 18.4 - - - +
14E CYS* 4.3 17.7 - - + +
95E THR* 3.7 32.3 - - + -
99E LEU* 4.0 20.6 - - + +
152E LYS* 1.3 71.9 - - - +
154E LEU* 1.3 62.8 + - - +
155E CYS* 4.0 3.3 + - + -
159E LEU* 4.6 20.9 - - + -
163E PHE* 5.7 0.9 - - + -
169E TRP* 5.2 3.1 - - + -
177E ILE* 4.4 8.5 - - + -
182E GLY 3.0 9.1 + - - +
183E LEU* 3.4 31.5 - - + +
184E ILE* 2.8 32.7 + - - +
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Residues in contact with LEU 154 (chain E).
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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11E LEU* 4.3 15.3 - - + -
12E LEU 2.8 23.6 + - - +
13E ALA* 3.7 14.6 - - + +
14E CYS 4.5 0.9 + - - -
27E LEU* 3.8 22.6 - - + +
28E PHE* 3.8 46.4 - - + -
31E ALA* 4.0 15.0 - - + -
152E LYS 3.4 0.8 + - - -
153E LEU* 1.3 74.9 - - - +
155E CYS* 1.3 74.5 + - - +
159E LEU* 5.4 0.3 - - - +
184E ILE* 3.4 15.3 - - + +
186E VAL* 3.9 23.8 - - + -
813E TAD 3.9 5.0 + - - -
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Residues in contact with CYS 155 (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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27E LEU* 4.6 6.3 - - - -
153E LEU* 4.7 2.9 - - + -
154E LEU* 1.3 78.1 - - - +
156E GLY* 1.3 64.1 + - - +
159E LEU* 3.8 26.5 - - + -
160E LEU 4.7 2.2 - - - -
183E LEU* 4.3 26.7 - - - -
184E ILE 2.9 14.6 + - - +
185E CYS* 3.2 15.2 - - - -
186E VAL* 2.8 34.5 + - - +
813E TAD 3.2 18.6 - - - +
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Residues in contact with GLY 156 (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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155E CYS* 1.3 83.2 - - - +
157E ALA* 1.3 65.1 + - - -
158E ASP 3.2 3.8 + - - -
159E LEU 3.3 8.1 + - - -
160E LEU 3.4 8.1 + - - -
185E CYS* 3.7 5.4 - - - -
186E VAL 3.2 11.7 - - - -
813E TAD 3.0 36.2 + - - -
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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