Contacts of the strand formed by residues 159 - 164 (chain C) in PDB entry 4AOR
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 159 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.6 21.1 - - + +
27C GLY 5.6 1.1 - - - -
28C TYR* 3.5 6.7 - - - +
29C THR* 3.4 31.5 + - - +
30C CYS* 3.2 8.6 - - - -
142C SER* 3.2 4.9 - - - -
143C GLY 3.0 37.0 + - - +
147C THR* 4.2 16.6 - - + -
155C PRO* 3.7 31.8 - - + +
156C ASP 5.4 0.2 - - - +
157C VAL* 3.5 24.5 - - - +
158C LEU* 1.3 79.4 - - - +
160C CYS* 1.3 59.5 + - - +
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Residues in contact with CYS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 4.1 2.0 - - - -
27C GLY* 3.1 5.7 - - - -
28C TYR* 2.8 62.1 + - + +
30C CYS* 2.1 44.4 - - - -
34C THR* 5.0 0.4 - - - -
35C VAL* 3.5 18.2 - - - -
140C LEU* 3.9 13.7 - - + -
141C ILE 3.6 4.0 - - - -
142C SER* 4.3 3.6 - - - -
159C LYS* 1.3 73.6 - - - +
161C LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.6 13.5 - - + -
25C VAL 4.3 0.4 - - - +
26C GLY 3.8 17.9 - - - +
27C GLY* 4.2 3.4 - - - -
28C TYR* 4.4 2.7 - - - -
139C CYS 3.6 0.3 - - - +
140C LEU* 3.5 8.5 - - - +
141C ILE* 2.8 48.2 + - + +
160C CYS* 1.3 76.1 - - - +
162C LYS* 1.3 77.5 + - - +
163C ALA* 3.8 16.5 + - + -
193C LYS* 3.8 29.6 - - + +
194C ASP* 3.5 38.8 - - - +
195C SER* 4.4 1.3 - - - +
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Residues in contact with LYS 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR* 4.2 20.4 + - + +
138C GLN* 4.3 15.3 - - + +
139C CYS 3.2 19.3 - - - +
140C LEU* 3.7 31.0 - - + -
161C LEU* 1.3 79.2 - - - +
163C ALA* 1.3 57.3 + - - +
188C TYR* 2.6 28.5 + - - +
193C LYS* 4.9 2.4 + - - -
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Residues in contact with ALA 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C GLN* 3.9 6.3 + - - -
139C CYS* 2.9 34.5 + - - +
141C ILE* 4.0 23.8 - - + -
161C LEU* 3.8 7.8 + - + -
162C LYS* 1.3 76.1 - - - +
164C PRO* 1.3 72.9 - - + +
186C ALA* 5.0 1.5 - - + +
187C GLY* 3.8 21.5 - - - +
188C TYR* 3.9 5.6 - - + -
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Residues in contact with PRO 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C GLY* 4.1 9.2 - - - +
137C THR 3.2 10.3 - - - +
138C GLN* 3.7 22.0 - - - +
163C ALA* 1.3 85.4 - - - +
165C ILE* 1.3 70.6 + - - +
166C LEU* 3.5 7.4 + - + +
186C ALA* 3.2 2.9 - - - -
187C GLY 2.9 43.8 + - - +
188C TYR* 3.6 24.0 - - + +
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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