Contacts of the strand formed by residues 155 - 160 (chain H) in PDB entry 1IB1
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 ARG 155 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H TRP* 5.1 0.8 - - - -
101H GLU 3.0 18.4 + - - -
102H GLU* 2.9 57.7 + - - +
117H HIS* 3.3 10.2 + - + +
118H SER* 3.3 25.2 + - - +
119H ALA 2.9 22.2 + - - -
153H VAL* 3.4 9.4 - - - +
154H ARG* 1.3 80.6 - - + +
156H ALA* 1.3 74.5 + - - +
157H VAL* 3.3 22.4 - - - +
192H HIS* 4.0 21.0 + - - -
193H CYS 3.2 20.2 - - - +
194H SER* 4.3 3.8 - - - +
195H LEU* 3.5 6.0 - - - +
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Residues in contact with ALA 156 (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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119H ALA* 3.3 13.9 - - + +
121H LEU* 4.2 4.9 - - + -
144H LEU* 3.9 27.8 - - + -
147H VAL* 5.7 0.2 - - + -
155H ARG* 1.3 74.9 - - - +
157H VAL* 1.3 68.2 + - - +
173H PHE* 3.8 8.7 - - + -
192H HIS* 3.5 0.7 - - - -
193H CYS* 2.8 43.2 + - + +
195H LEU* 4.3 7.0 - - + -
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Residues in contact with VAL 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H TRP* 4.9 3.4 - - + -
102H GLU 4.9 0.4 - - - +
104H LEU* 4.1 22.7 - - + -
118H SER* 4.3 10.1 - - - -
119H ALA 2.9 9.5 + - - +
120H HIS* 3.4 27.0 - - + +
121H LEU* 2.8 28.5 + - - +
155H ARG* 3.3 37.9 - - - +
156H ALA* 1.3 75.6 - - - +
158H LEU* 1.3 62.1 + - - +
173H PHE* 4.5 0.4 - - - -
190H GLU* 5.2 0.4 - - - +
191H MET 3.4 5.4 - - - +
192H HIS* 3.3 22.9 - - + +
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Residues in contact with LEU 158 (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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104H LEU* 4.4 9.1 - - - +
120H HIS* 4.8 0.7 - - - -
121H LEU* 3.8 35.0 - - + +
124H LEU* 5.6 0.4 - - + -
157H VAL* 1.3 77.9 - - - +
159H MET* 1.3 70.6 + - - +
168H TYR* 3.8 42.2 - - + +
173H PHE* 3.6 34.3 - - + -
190H GLU* 3.7 3.3 - - - +
191H MET* 2.8 54.1 + - + +
403H COT 4.6 4.9 - - + -
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Residues in contact with MET 159 (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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104H LEU* 4.6 1.9 - - + +
109H LEU* 3.6 31.4 - - + -
120H HIS* 4.6 10.3 - - - +
121H LEU 4.9 2.8 + - - +
122H HIS* 5.3 3.4 - - - +
158H LEU* 1.3 77.8 - - - +
160H CYS* 1.3 62.9 + - - +
179H CYS* 3.8 20.0 - - - -
181H ILE* 3.8 29.2 - - + -
183H VAL* 5.2 0.2 - - + -
188H PHE* 3.7 31.9 - - + -
189H THR 3.3 10.8 - - - +
403H COT 2.9 58.9 + - + +
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Residues in contact with CYS 160 (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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158H LEU* 4.2 0.4 - - + -
159H MET* 1.3 76.7 - - - +
161H GLU* 1.3 69.7 + - - +
164H LEU* 4.0 2.9 - - + -
165H VAL* 3.8 22.7 - - - -
168H TYR* 3.6 29.6 - - + -
188H PHE* 3.2 10.3 - - - +
189H THR* 2.7 33.5 + - - +
191H MET* 4.0 13.5 - - - -
403H COT 3.5 23.8 - - - -
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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