Contacts of the strand formed by residues 111 - 116 (chain A) in PDB entry 5P21
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 MET 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.2 17.5 - - + +
80A CYS* 3.7 23.6 - - - -
97A ARG* 3.5 42.4 - - - +
100A ILE* 3.8 40.6 - - + -
101A LYS* 5.9 1.8 - - + -
109A VAL* 3.1 20.4 + - + +
110A PRO* 1.3 71.7 - - - +
112A VAL* 1.3 67.2 + - - +
137A TYR* 5.5 0.4 - - - -
139A ILE* 3.5 36.5 - - + +
140A PRO* 3.5 8.8 - - - +
159A LEU* 3.9 3.1 - - - +
162A GLU* 4.6 5.7 + - - +
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Residues in contact with VAL 112 (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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78A PHE 3.0 5.7 + - - -
79A LEU* 3.7 14.3 - - + -
80A CYS* 3.0 26.7 + - - +
111A MET* 1.3 79.1 - - - +
113A LEU* 1.3 70.5 + - - +
114A VAL* 3.8 14.4 + - + +
139A ILE* 4.2 3.8 - - - -
140A PRO* 3.8 16.2 - - + +
142A ILE* 4.2 23.1 - - + -
155A ALA 4.3 2.2 - - - +
158A THR* 4.1 12.8 - - + -
159A LEU* 3.8 36.8 - - + +
162A GLU* 4.6 2.0 - - + -
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Residues in contact with LEU 113 (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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80A CYS* 3.6 17.3 - - + +
82A PHE* 3.9 25.6 - - + -
93A ILE* 3.9 26.7 - - + -
112A VAL* 1.3 71.4 - - - +
114A VAL* 1.3 58.5 + - - +
130A ALA* 3.7 24.7 - - + +
133A LEU* 4.3 14.8 - - + -
134A ALA* 3.9 16.8 - - + +
137A TYR* 5.4 1.3 - - + -
139A ILE* 3.8 16.5 - - + +
140A PRO 3.0 14.7 + - - +
141A TYR* 3.4 14.9 - - + -
142A ILE 2.9 26.7 + - - -
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Residues in contact with VAL 114 (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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19A LEU* 4.1 16.4 - - + -
79A LEU* 4.1 17.5 - - + -
80A CYS 2.9 12.5 + - - +
81A VAL* 4.3 7.9 - - + -
82A PHE* 2.9 34.2 + - - +
112A VAL* 3.9 20.6 - - + +
113A LEU* 1.3 77.3 - - - +
115A GLY* 1.3 62.1 + - - +
116A ASN 4.3 1.3 - - - +
142A ILE* 3.2 5.8 - - + +
144A THR* 3.5 35.4 - - + +
155A ALA* 3.9 17.3 - - + -
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Residues in contact with GLY 115 (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 PHE* 3.6 28.0 - - - -
84A ILE* 4.1 6.2 - - - +
114A VAL* 1.3 72.5 - - - +
116A ASN* 1.3 61.2 + - - -
118A CYS* 4.5 1.0 - - - +
141A TYR* 3.8 12.3 - - - -
142A ILE 2.9 11.1 + - - -
143A GLU* 3.3 8.8 - - - +
144A THR* 2.9 24.0 + - - +
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Residues in contact with ASN 116 (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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14A VAL 2.9 23.7 + - - +
15A GLY* 3.7 8.1 + - - -
19A LEU* 3.5 11.9 - - + +
81A VAL* 4.0 12.6 - - + -
82A PHE 2.7 18.4 + - - +
83A ALA* 3.5 1.2 - - - -
84A ILE* 3.0 24.0 + - - +
114A VAL* 3.6 0.6 + - + -
115A GLY* 1.3 71.9 - - - +
117A LYS* 1.4 81.9 + - - +
118A CYS 3.3 2.5 - - - -
144A THR* 2.7 27.5 + - - +
146A ALA* 3.4 15.8 + - - +
167A GNP 3.2 24.4 + - - -
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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