Contacts of the strand formed by residues 105 - 109 (chain B) in PDB entry 2PI8
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 VAL 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLN* 5.5 3.3 - - - +
168A ASP* 5.3 1.6 - - - +
170A GLY* 3.6 37.7 - - - +
172A GLY 4.5 0.9 - - - +
103B THR 4.5 0.4 - - - +
104B PRO* 1.3 73.8 - - - +
106B ILE* 1.3 62.2 + - - +
107B GLN 4.0 1.4 + - - -
155B ASP* 5.7 0.3 - - - +
166B TYR* 3.3 8.5 - - + +
168B ASP* 3.9 21.1 - - + -
175B LEU* 3.8 28.7 - - + -
313B ILE* 3.9 25.4 - - + -
314B GLY* 4.5 4.6 - - - +
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PRO* 4.6 12.1 - - + +
105B VAL* 1.3 76.3 - - - +
107B GLN* 1.3 64.6 + - - +
108B ALA* 3.6 1.1 + - + -
120B ILE* 4.8 0.9 - - + -
150B SER* 3.6 29.8 - - - -
151B ASN* 5.1 0.9 - - - +
155B ASP* 3.2 51.6 - - + +
156B ASN* 4.0 2.0 - - - +
159B MSE 3.5 35.9 - - + -
166B TYR 2.9 9.5 + - - +
167B ILE* 3.5 20.1 - - + +
168B ASP* 2.9 28.3 + - - +
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLN* 3.2 30.1 + - - +
151A ASN* 5.5 2.6 + - - -
105B VAL 4.0 2.2 + - - -
106B ILE* 1.3 72.9 - - - +
108B ALA* 1.3 63.8 + - - +
109B ARG* 3.6 22.6 - - - +
116B PHE* 3.4 22.6 - - + -
150B SER* 3.4 18.5 - - - -
151B ASN* 3.5 33.8 + - - +
155B ASP* 5.6 1.0 + - - -
168B ASP* 3.4 16.4 - - + +
170B GLY* 5.7 1.5 - - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 3.6 1.1 + - + +
107B GLN* 1.3 76.2 - - - +
109B ARG* 1.3 80.6 + - - +
116B PHE* 3.9 2.7 - - - -
120B ILE* 4.8 4.0 - - + -
148B ALA* 3.9 17.9 - - + -
149B TYR 3.2 22.9 - - - +
150B SER* 3.9 5.4 - - - +
167B ILE* 3.9 15.5 - - + -
168B ASP 3.0 7.1 + - - -
169B PHE* 3.3 20.5 - - - -
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A PRO* 3.4 38.1 - - - +
316A GLU* 6.1 2.7 - - - -
107B GLN* 3.6 23.2 - - - +
108B ALA* 1.3 90.9 + - - +
110B HIS* 1.3 63.1 + - - +
111B THR 3.2 19.0 + - - +
113B GLN* 4.3 17.6 + - + +
116B PHE* 3.4 53.0 - - + -
148B ALA* 3.5 2.4 - - - -
149B TYR* 2.9 32.6 + - - +
169B PHE* 3.4 26.7 + - - -
170B GLY* 4.4 3.4 + - - +
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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