Contacts of the strand formed by residues 158 - 163 (chain N) in PDB entry 2QKK
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 158 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147N CYS 3.1 10.1 - - - +
148N CYS* 4.0 2.5 - - - +
157N ARG* 1.3 71.5 - - - +
159N GLY* 1.3 59.5 + - - +
175N ARG* 3.4 12.8 + - - +
176N LEU* 2.9 50.2 + - + -
180N GLN* 3.1 31.9 - - + +
181N THR 4.1 6.3 - - - +
185N ALA* 4.2 3.1 - - + -
280N GLY 4.8 0.2 - - - -
281N ALA* 5.2 2.2 - - - -
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Residues in contact with GLY 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146N GLY* 3.5 4.0 - - - -
147N CYS* 2.8 37.3 + - - +
157N ARG 3.9 0.2 + - - -
158N ALA* 1.3 75.3 - - - +
160N ILE* 1.3 66.0 + - - +
174N ILE 3.7 7.2 - - - -
176N LEU 4.5 0.2 - - - -
185N ALA* 3.8 1.3 - - - +
277N ALA* 3.4 20.9 - - - +
280N GLY* 4.1 7.2 - - - -
281N ALA* 4.6 1.5 - - - +
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Residues in contact with ILE 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145N ASP 4.6 0.9 - - - -
159N GLY* 1.3 77.5 - - - +
161N GLY* 1.3 66.5 + - - +
162N VAL* 5.1 2.7 - - + -
172N VAL* 3.8 1.4 - - + +
173N GLY* 3.5 5.2 - - - -
174N ILE* 3.0 50.1 + - + +
175N ARG* 4.8 2.0 - - - +
176N LEU* 3.6 23.3 - - + -
177N PRO* 5.2 1.6 - - + -
185N ALA* 4.1 16.2 - - + +
188N HIS* 3.6 38.8 - - + +
189N ALA* 3.3 24.9 - - + +
192N LYS* 4.8 9.6 - - + -
277N ALA* 3.4 6.3 + - - -
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Residues in contact with GLY 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143N TYR 4.3 0.4 - - - -
144N THR* 3.6 2.6 - - - -
145N ASP 3.4 24.5 + - - -
160N ILE* 1.3 83.1 - - - +
162N VAL* 1.3 67.1 + - - +
172N VAL 3.6 6.3 - - - -
189N ALA* 3.9 2.3 - - - +
273N ALA* 3.8 8.1 - - - -
276N LEU* 4.6 0.7 - - - -
277N ALA* 3.0 26.9 - - - +
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Residues in contact with VAL 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142N VAL* 3.6 14.1 - - + -
143N TYR 3.0 8.3 - - - +
144N THR* 4.9 0.2 - - - -
160N ILE* 5.1 3.1 - - + -
161N GLY* 1.3 76.3 - - - +
163N TYR* 1.3 59.3 + - - +
164N TRP* 3.7 9.5 + - - +
170N LEU 4.8 0.4 - - - +
171N ASN* 3.4 6.1 - - - +
172N VAL* 3.2 53.2 + - + +
189N ALA 4.4 5.6 - - - +
192N LYS* 4.5 11.0 - - + -
193N ALA* 3.2 35.9 - - + -
196N GLN* 3.9 6.7 - - - +
273N ALA* 4.4 1.4 - - - +
276N LEU* 4.1 4.0 - - - +
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Residues in contact with TYR 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142N VAL* 3.8 0.4 - - - -
143N TYR* 2.8 52.1 + + + -
162N VAL* 1.3 72.1 - - - +
164N TRP* 1.3 60.4 + - - +
165N GLY* 3.3 28.7 - - - -
166N PRO* 3.1 27.5 - - + +
171N ASN* 3.3 20.9 - - - +
268N ILE* 5.8 0.5 - - - +
269N GLY* 4.0 13.0 + - - -
272N GLU* 3.3 49.6 + - + +
273N ALA* 4.1 21.3 - - + +
276N LEU* 4.6 4.0 - - + -
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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