Contacts of the strand formed by residues 158 - 162 (chain H) in PDB entry 2Q5E
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 GLU 158 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H LEU* 5.2 1.0 - - - +
94H VAL* 3.7 18.8 - - - +
95H THR* 5.3 1.0 + - - +
98H ASP* 3.9 32.6 - - + +
101H ARG* 3.8 10.5 - - + +
102H ILE 3.0 13.0 + - - +
103H CYS* 3.4 14.5 + - - +
104H VAL* 2.7 32.9 + - - +
157H PHE* 1.3 71.4 - - - +
159H CYS* 1.3 56.3 + - - +
160H VAL* 4.7 9.7 - - + +
208H ARG* 2.9 44.9 + - - -
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Residues in contact with CYS 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H VAL* 3.5 5.4 - - - -
106H ILE* 4.4 8.7 - - + -
150H LEU* 6.0 0.2 - - - -
153H MET* 3.5 39.5 - - - -
154H GLY* 4.0 1.8 - - - -
157H PHE* 3.6 8.8 + - - -
158H GLU* 1.3 75.5 - - - +
160H VAL* 1.3 62.9 + - - +
182H VAL* 3.4 50.6 + - + +
183H PHE* 3.6 20.6 - - + -
184H ARG 3.7 5.4 + - - -
185H ALA 4.4 0.9 + - - +
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Residues in contact with VAL 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H LEU* 4.2 10.3 - - + -
103H CYS* 3.6 26.2 - - - -
104H VAL 2.8 12.2 + - - +
105H VAL* 3.5 14.3 - - + -
106H ILE* 2.9 27.4 + - - +
158H GLU* 4.4 9.9 - - + +
159H CYS* 1.3 78.2 - - - +
161H LEU* 1.3 73.8 + - - +
162H PHE* 3.3 0.6 + - + +
183H PHE* 3.8 3.7 - - - -
185H ALA* 3.6 27.8 - - + +
187H LEU* 4.1 22.7 - - + -
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Residues in contact with LEU 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ILE 3.4 13.7 - - - +
107H ASP 4.3 1.8 - - - +
108H LEU* 4.1 28.9 - - + +
112H LEU* 5.2 0.9 - - + -
160H VAL* 1.3 74.3 - - - +
162H PHE* 1.3 59.4 + - - +
163H THR* 3.9 11.7 - - + -
170H ALA* 4.8 2.7 - - + -
174H THR* 3.5 24.7 - - + +
183H PHE* 3.4 35.2 - - + -
185H ALA 3.2 7.1 + - - -
186H ARG* 4.2 18.8 - - + -
187H LEU* 2.9 27.2 + - - +
188H PHE* 4.1 25.8 - - + -
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Residues in contact with PHE 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H LEU* 4.2 9.4 - - + -
105H VAL* 3.5 36.3 - - + -
106H ILE 2.8 11.0 + - - +
107H ASP* 3.6 12.8 + - - -
160H VAL* 3.3 1.5 + - + +
161H LEU* 1.3 74.6 - - - +
163H THR* 1.3 63.1 + - - +
187H LEU* 3.7 20.9 - - + -
188H PHE 4.2 0.9 - - - -
191H SER* 3.4 38.4 - - - -
192H CYS* 3.7 22.0 - - - -
201H LYS* 3.1 53.4 + - + -
202H ASP 4.8 1.8 - - - -
203H LEU* 4.8 2.5 - - + -
206H LEU* 4.1 21.3 - - + -
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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