Contacts of the strand formed by residues 134 - 138 (chain E) in PDB entry 2P1N
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 134 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E GLU 3.0 2.8 + - - -
109E GLU* 3.3 28.8 - - + +
110E ILE 2.8 33.1 + - - +
111E ARG* 3.9 29.6 - - - +
132E PHE* 3.3 8.2 - - - -
133E LYS* 1.3 85.6 - - + +
135E LEU* 1.3 58.6 + - - +
136E VAL* 4.0 18.2 - - + +
159E LYS* 5.1 4.0 - - + -
160E GLU* 3.7 34.3 - - + +
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Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ILE* 3.6 22.4 - - + +
112E LEU* 5.4 0.2 - - + -
122E LEU* 3.8 28.9 - - + -
125E ILE* 5.4 4.3 - - + -
132E PHE* 3.8 20.1 - - + -
134E VAL* 1.3 69.9 - - - +
136E VAL* 1.3 63.7 + - - +
137E LEU* 4.0 30.5 - - + -
148E LEU* 5.6 1.1 - - + -
151E ILE* 4.3 17.3 - - + -
158E LEU* 4.6 2.9 - - + +
160E GLU 2.9 15.7 + - - +
161E LEU* 3.5 22.7 - - + +
162E ASP 2.9 25.3 + - - +
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Residues in contact with VAL 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E ILE 3.1 7.5 + - - +
111E ARG* 3.4 35.6 - - + +
112E LEU 2.9 28.8 + - - +
134E VAL* 4.0 17.5 - - + -
135E LEU* 1.3 74.5 - - - +
137E LEU* 1.3 64.1 + - - +
138E SER* 4.3 18.2 - - - -
160E GLU* 4.5 7.4 - - + +
162E ASP* 3.4 27.4 - - + +
164E ARG* 4.5 18.2 - - - +
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Residues in contact with LEU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E LEU* 3.8 31.9 - - + -
117E VAL* 4.1 19.3 - - + -
122E LEU* 4.4 10.5 - - + -
135E LEU* 4.0 30.5 - - + -
136E VAL* 1.3 75.4 - - - +
138E SER* 1.3 61.7 + - - +
140E CYS* 4.1 4.0 - - + -
143E PHE* 3.5 33.4 - - + -
148E LEU* 5.1 0.7 - - + -
162E ASP 2.7 12.0 + - - +
163E LEU* 3.1 16.6 - - + -
164E ARG 3.0 24.1 + - - -
166E SER* 3.1 17.1 + - - +
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Residues in contact with SER 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E LEU 2.9 15.8 + - - +
113E LYS* 3.3 27.4 - - - +
114E ARG 3.1 15.8 + - - -
136E VAL* 4.3 11.2 - - - -
137E LEU* 1.3 73.9 - - - +
139E SER* 1.3 71.4 + - - +
140E CYS* 3.2 2.1 + - - -
164E ARG* 3.4 29.4 + - - +
165E GLU* 5.5 1.4 - - - +
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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