Contacts of the strand formed by residues 172 - 175 (chain A) in PDB entry 2POD
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 ALA 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ARG* 3.5 23.6 - - - +
117A THR 4.5 2.3 + - - +
118A TYR* 3.3 23.9 - - + -
119A ASN 2.9 22.2 + - - -
170A ILE* 3.4 10.2 - - - +
171A THR* 1.3 81.4 - - - +
173A MSE 1.3 61.5 + - - +
213A MSE 3.6 3.7 - - - -
214A ASP* 3.3 12.1 - - + +
216A MSE 3.9 10.5 - - + -
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Residues in contact with MSE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 4.6 1.1 - - - -
119A ASN 3.2 11.7 - - - +
121A CYS* 4.0 3.4 - - - -
154A PHE* 5.0 1.6 - - + -
158A ALA* 4.8 4.3 - - + +
161A LEU* 3.9 29.4 - - + -
162A ALA* 4.2 18.2 - - - -
165A LEU* 4.0 14.4 - - + -
172A ALA* 1.3 74.9 - - - +
174A LYS* 1.3 59.5 + - - +
175A ILE* 3.8 24.7 - - + -
205A ILE* 4.5 20.0 - - + -
213A MSE 3.7 32.3 - - + +
214A ASP 2.9 9.1 + - - +
215A VAL* 3.5 11.4 - - + +
216A MSE 2.8 30.4 + - - +
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 3.2 29.6 + - + -
119A ASN 2.9 8.5 + - - -
120A THR* 3.5 15.9 - - - +
121A CYS* 3.2 22.7 + - - +
173A MSE 1.3 75.0 - - - +
175A ILE* 1.3 68.2 + - - +
176A TRP* 3.5 7.9 - - + -
216A MSE 3.4 21.3 - - + +
218A GLU* 3.9 28.5 - - + +
242A TRP* 4.3 1.3 - - - +
244A GLU* 2.8 38.1 + - - +
291A MSE 4.5 1.8 - - - -
345A GLU* 2.9 28.7 + - - -
409A NA 3.6 4.8 - - - -
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A CYS* 4.3 2.5 - - - -
154A PHE* 3.6 34.5 - - + -
158A ALA* 6.1 0.7 - - + -
173A MSE 3.8 24.2 - - + -
174A LYS* 1.3 79.9 - - - +
176A TRP* 1.3 66.7 + - - +
177A PRO* 3.7 9.3 - - + +
201A PRO* 3.9 27.6 - - + +
202A PHE* 3.7 30.1 - - + -
205A ILE* 6.0 2.9 - - + -
215A VAL* 4.1 11.7 - - + -
216A MSE 3.1 11.7 + - - +
217A VAL* 3.6 2.6 - - - -
218A GLU 3.0 22.3 + - - -
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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