Contacts of the helix formed by residues 158 - 161 (chain I) in PDB entry 2WQT
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 ASN 158 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I GLN* 3.2 22.7 - - + +
46I VAL* 5.1 3.4 - - - -
81I THR* 2.7 49.8 + - - -
83I PHE* 4.8 8.3 - - - -
86I MET* 5.0 2.2 - - - +
143I ARG* 4.9 2.5 - - - +
155I VAL 3.0 7.4 + - - -
156I ALA 3.0 8.5 + - - +
157I ASP* 1.3 77.3 - - - +
159I ALA* 1.3 67.8 + - - +
161I CYS* 3.1 29.1 + - + +
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Residues in contact with ALA 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I GLN* 4.0 0.4 - - - +
60I LYS* 3.0 32.9 + - + -
78I ASP* 3.6 19.6 - - - +
79I PHE* 3.5 21.3 - - - +
80I GLY* 3.6 11.4 - - - +
154I THR* 2.8 30.1 + - - +
155I VAL 3.5 4.6 + - - -
158I ASN* 1.3 72.5 - - - +
160I SER* 1.3 62.0 + - - +
1262I PO4 4.2 1.6 + - - -
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Residues in contact with SER 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I VAL* 3.2 13.7 - - - +
141I GLY 2.9 39.0 + - - -
142I SER* 4.9 3.0 + - - -
143I ARG* 3.7 0.9 - - - +
147I TRP* 3.9 23.3 - - - -
149I ILE* 4.9 3.6 - - - +
154I THR* 2.5 36.2 + - - +
157I ASP* 3.1 15.8 + - - +
159I ALA* 1.3 76.1 - - - +
161I CYS* 1.3 59.7 + - - +
1262I PO4 5.2 1.8 - - - -
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Residues in contact with CYS 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I LYS* 3.7 18.2 - - - -
80I GLY* 4.6 2.9 - - - -
81I THR 4.2 2.0 - - - -
82I LEU* 4.0 11.2 - - - -
86I MET* 3.6 25.1 - - + -
138I GLU* 3.7 19.3 - - - -
141I GLY 4.1 0.9 - - - -
143I ARG* 2.9 29.7 + - - +
158I ASN* 3.1 38.3 + - + +
159I ALA 3.3 0.8 - - - -
160I SER* 1.3 76.9 - - - +
162I GLY* 1.3 59.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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