Contacts of the strand formed by residues 166 - 173 (chain A) in PDB entry 5KC6
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 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ASP* 5.5 0.6 + - - -
101A ARG* 4.1 20.6 - - - +
103A THR* 3.6 36.6 + - + +
104A PHE 3.5 3.8 - - - -
105A ILE* 3.7 24.7 - - + +
132A MET 3.5 0.9 - - - +
133A LEU* 3.4 9.6 - - - +
134A ASN* 2.7 44.4 + - - +
164A GLY 3.8 10.1 - - - +
165A ASP* 1.3 75.6 - - - +
167A ALA* 1.3 59.8 + - - +
168A TYR* 4.3 13.3 - - + -
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Residues in contact with ALA 167 (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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102A SER 4.3 0.3 - - - +
103A THR* 3.3 1.6 - - - +
104A PHE* 2.7 45.8 + - + +
114A PHE* 3.8 35.7 - - + -
131A LEU* 4.6 7.0 - - + -
132A MET 3.3 9.0 - - - +
133A LEU* 5.0 2.0 - - + -
159A ILE* 5.6 1.8 - - + -
161A MET* 4.1 8.7 - - + -
166A ARG* 1.3 74.6 - - - +
168A TYR* 1.3 63.9 + - - +
185A PHE* 4.6 4.0 - - + -
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Residues in contact with TYR 168 (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 ILE* 4.1 29.6 - - + -
102A SER 3.5 19.3 - - - +
103A THR* 3.8 19.7 - - + +
131A LEU* 3.6 4.3 - - - +
132A MET* 2.7 64.1 + - + +
134A ASN* 5.1 0.2 - - - -
135A GLY* 3.3 32.6 + - - -
166A ARG* 4.3 16.6 - - + -
167A ALA* 1.3 83.6 - - - +
169A LEU* 1.3 73.8 + - - +
170A LYS* 4.5 9.0 - - + +
185A PHE* 4.2 6.5 - - - -
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Residues in contact with LEU 169 (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 ILE* 3.5 10.8 - - - +
84A ILE* 3.0 41.4 + - + +
86A PHE* 3.6 31.0 - - + -
102A SER 4.8 1.0 + - - -
116A PHE* 3.6 50.9 - - + -
118A VAL* 4.3 7.9 - - + -
129A VAL* 4.2 1.8 - - + -
130A SER 3.5 3.8 - - - +
131A LEU* 3.8 27.6 - - + +
168A TYR* 1.3 77.7 - - - +
170A LYS* 1.3 60.7 + - - +
185A PHE* 3.8 20.2 - - + -
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Residues in contact with LYS 170 (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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81A THR 4.2 6.5 - - - +
82A MET* 3.2 50.3 - - + +
83A ILE* 4.6 3.1 - - + +
84A ILE* 4.3 4.0 - - - -
129A VAL* 3.5 2.1 - - - +
130A SER* 2.9 32.7 + - - -
132A MET* 3.7 33.0 - - + +
168A TYR* 4.1 9.1 + - + +
169A LEU* 1.3 74.9 - - - +
171A LEU* 1.3 59.9 + - - +
172A GLU* 2.8 36.3 + - - +
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Residues in contact with LEU 171 (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 MET* 2.7 40.1 + - + +
84A ILE* 4.2 13.2 - - + +
127A ILE* 4.1 11.9 - - + -
128A GLN 3.7 3.6 - - - +
129A VAL* 3.9 23.3 - - + -
170A LYS* 1.3 69.0 - - - +
172A GLU* 1.3 63.7 + - - +
173A ARG* 3.4 17.2 + - - +
174A GLY 3.2 22.5 - - - +
175A ASN* 3.6 16.6 - - - -
176A LEU* 4.0 24.9 - - + +
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Residues in contact with GLU 172 (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 MET* 5.7 2.6 - - - +
128A GLN* 2.7 37.9 + - + +
130A SER* 3.3 34.8 + - - +
132A MET* 3.7 16.2 - - + +
137A PRO* 4.1 11.3 - - - +
140A SER* 4.8 0.3 + - - -
170A LYS* 2.8 32.9 + - - +
171A LEU* 1.3 72.8 - - - +
173A ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 173 (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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126A THR* 3.8 20.1 + - - +
127A ILE* 3.3 19.4 - - - -
128A GLN* 3.3 43.8 + - + +
142A PHE* 4.9 10.4 - - - -
171A LEU* 3.3 10.0 - - - +
172A GLU* 1.3 81.3 - - + +
174A GLY* 1.3 69.7 + - - +
148B VAL 6.0 0.6 + - - -
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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