Contacts of the strand formed by residues 155 - 159 (chain A) in PDB entry 4PIM
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA* 4.0 3.1 - - - -
81A THR* 3.4 15.5 - - + +
83A VAL* 4.2 20.2 - - + +
110A ILE* 4.8 0.4 - - - -
149A ILE* 3.5 22.8 + - - +
150A PRO 3.0 30.0 + - - -
151A HIS* 3.5 15.9 + - - +
152A VAL 3.8 16.6 - - - +
153A GLY 3.8 8.0 + - - +
154A ARG* 1.3 76.9 - - - +
156A LEU* 1.3 58.8 + - - +
157A VAL* 3.8 9.2 + - + +
182A THR* 3.0 29.9 + - - -
183A LEU* 4.2 5.3 - - - +
184A GLN* 3.1 6.9 + - - -
186A GLY 4.5 0.4 - - - +
187A ASP* 2.9 43.2 + - + +
188A SER* 2.9 26.4 + - - +
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Residues in contact with LEU 156 (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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73A ILE* 4.7 8.1 - - + -
74A ILE* 3.9 28.7 - - + -
77A ALA* 4.1 11.0 - - + -
79A ALA* 3.6 18.0 - - + +
81A THR 2.9 10.7 + - - +
82A LEU* 3.5 21.2 - - + +
83A VAL 2.8 26.9 + - - +
96A LEU* 4.8 3.4 - - + -
100A MSE 4.9 3.1 - - - -
155A ARG* 1.3 70.0 - - - +
157A VAL* 1.3 61.5 + - - +
158A VAL* 3.8 11.4 - - + -
188A SER* 3.6 15.0 - - - +
190A LEU* 4.1 12.3 - - + -
318A LEU* 3.9 26.9 - - + -
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Residues in contact with VAL 157 (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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83A VAL* 3.4 29.4 - - + +
85A LEU* 4.0 30.7 - - + -
149A ILE* 5.8 1.6 - - + -
155A ARG* 4.6 15.3 - - + +
156A LEU* 1.3 73.5 - - - +
158A VAL* 1.3 63.1 + - - +
179A LEU* 4.3 14.4 - - + -
182A THR* 5.9 0.2 - - - +
183A LEU* 3.9 26.2 - - + -
188A SER 2.8 12.3 + - - +
189A LEU* 3.3 13.0 - - + +
190A LEU* 2.8 24.9 + - - -
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Residues in contact with VAL 158 (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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82A LEU* 3.5 28.7 - - + -
83A VAL 2.8 19.0 + - - +
84A GLU* 3.8 22.7 - - + -
85A LEU* 3.0 31.7 + - - +
93A THR* 6.6 0.2 - - - -
96A LEU* 4.1 7.9 - - + -
156A LEU* 3.8 12.1 - - + -
157A VAL* 1.3 79.5 - - - +
159A PHE* 1.3 59.3 + - - +
160A LEU* 4.3 21.5 - - + -
190A LEU* 3.4 23.8 - - + +
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Residues in contact with PHE 159 (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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85A LEU* 3.5 38.4 - - + -
142A PHE* 4.0 27.6 - + - -
157A VAL 4.3 0.2 + - - -
158A VAL* 1.3 73.6 - - - +
160A LEU* 1.3 63.0 + - - +
163A THR* 3.7 37.8 + - + -
164A ILE* 3.7 22.1 + - + -
167A LEU* 5.3 0.9 - - + -
175A PHE* 3.5 35.2 - + - -
179A LEU* 5.5 0.2 - - + -
189A LEU* 4.6 6.5 - - + -
190A LEU 2.9 9.6 + - - +
191A LEU* 3.6 29.3 - - + +
192A GLY 3.0 22.9 + - - +
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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