Contacts of the strand formed by residues 151 - 161 (chain C) 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 GLU 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A THR* 4.8 5.0 - - - +
142B PHE 6.0 0.7 - - - -
118C VAL 3.9 0.7 - - - +
119C VAL* 3.7 3.8 - - - -
120C LYS* 3.2 33.9 + - + +
143C ALA* 4.2 7.8 - - + +
144C GLY* 2.7 47.4 + - - +
146C GLN* 2.4 34.8 + - - +
149C THR* 5.1 2.7 - - + +
150C ARG* 1.3 74.9 - - - +
152C ALA* 1.3 61.7 + - - +
153C ALA 4.3 0.2 + - - -
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B SER 5.4 4.7 - - - +
117C HIS* 4.6 6.7 - - + +
118C VAL 3.3 10.5 - - - +
119C VAL* 4.1 17.7 - - + -
142C PHE 3.8 7.6 - - - +
143C ALA* 4.3 2.1 - - - +
151C GLU* 1.3 76.3 - - - +
153C ALA* 1.3 60.0 + - - +
154C SER* 3.4 22.1 + - - +
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Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PHE* 3.6 12.1 - - - -
118C VAL* 3.0 31.6 + - - +
127C ILE* 4.5 4.0 - - + -
129C VAL* 4.3 17.9 - - + -
141C ALA* 3.4 18.6 - - + +
142C PHE 3.3 29.1 + - - +
143C ALA* 4.0 7.4 - - + +
152C ALA* 1.3 69.1 - - - +
154C SER* 1.3 57.8 + - - +
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Residues in contact with SER 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A HIS* 3.5 17.9 + - - +
154A SER* 5.9 0.9 - - - -
154B SER* 6.3 0.4 - - - -
116C PHE 3.3 4.5 - - - -
117C HIS* 2.8 38.9 + - - -
141C ALA* 3.4 10.0 - - - +
152C ALA* 3.4 21.7 + - - +
153C ALA* 1.3 76.5 - - - +
155C ASN* 1.3 65.6 + - - +
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Residues in contact with ASN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A HIS* 3.3 22.6 - - - +
119A VAL* 5.2 2.2 - - - +
182A TYR 3.7 7.3 + - - -
184A THR* 2.8 42.5 + - - +
115C ASN* 3.7 2.9 - - - +
116C PHE* 3.3 47.1 + - + +
117C HIS* 5.5 1.7 + - - -
139C ILE* 3.9 16.3 - - + +
140C SER 3.1 24.6 + - - +
141C ALA* 4.2 0.4 - - + +
154C SER* 1.3 77.1 + - - +
156C GLY* 1.3 75.6 + - - +
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Residues in contact with GLY 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASN* 6.0 3.7 - - - +
117A HIS* 3.8 7.2 + - - -
184A THR* 3.7 11.4 + - - -
186A SER* 4.3 7.2 + - - -
114C PHE 3.2 14.4 - - - -
115C ASN* 3.8 10.1 - - - -
139C ILE* 3.7 6.1 - - - +
155C ASN* 1.3 93.6 + - - +
157C VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER* 3.0 25.4 - - - +
66A ALA 5.9 0.2 - - - +
67A ILE* 5.0 3.4 - - + -
90A LEU* 3.7 21.3 - - + -
184A THR* 5.6 2.2 - - + -
186A SER* 4.2 6.9 + - - -
112C TYR 3.8 0.9 - - - +
113C SER* 3.7 2.1 + - - -
114C PHE* 3.0 31.8 + - + +
131C LEU* 3.6 21.5 - - + -
138C VAL* 4.1 3.6 - - + -
139C ILE* 3.5 28.3 - - + -
156C GLY* 1.3 76.1 - - - +
158C LEU* 1.3 70.1 + - - +
159C ILE* 4.0 13.1 + - + -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA* 3.9 17.3 - - + -
64A PHE 3.6 10.3 - - - +
65A SER* 3.1 24.3 + - - +
90A LEU* 4.2 1.2 - - - +
91A VAL* 3.1 14.7 - - + +
186A SER* 4.4 6.0 - - - +
187A GLY 3.5 28.0 - - - +
188A PHE* 3.9 20.0 - - + -
111C ILE* 4.2 8.7 - - + -
112C TYR 3.3 4.9 - - - +
113C SER* 3.4 35.7 - - - +
157C VAL* 1.3 78.2 - - - +
159C ILE* 1.3 65.8 + - - +
190C VAL* 3.8 15.0 - - + -
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 4.3 8.1 - - + -
91A VAL* 3.7 7.4 - - - -
111C ILE* 3.7 2.6 - - - -
112C TYR* 3.0 28.0 + - - +
114C PHE* 3.6 37.2 - - + -
131C LEU* 4.8 6.1 - - + -
132C MET 5.8 0.2 - - - +
133C LEU* 4.2 23.3 - - + -
138C VAL* 3.6 37.2 - - + -
157C VAL* 4.0 8.3 - - + -
158C LEU* 1.3 79.9 - - - +
160C GLN* 1.3 63.6 + - - +
161C MET* 3.7 15.4 + - + -
167C ALA* 5.4 2.5 - - + -
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Residues in contact with GLN 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 5.2 3.5 + - - +
91A VAL* 4.0 8.9 - - + +
93A ILE* 4.8 6.2 - - - +
109C LYS* 4.6 7.9 - - + +
110C GLY 3.5 11.7 - - - +
111C ILE* 3.7 14.4 - - + +
133C LEU* 4.2 14.6 - - - +
159C ILE* 1.3 73.0 - - - +
161C MET* 1.3 72.1 + - - +
162C GLU* 3.6 19.7 + - + +
165C ASP* 4.8 0.3 - - - +
193C LEU* 3.7 22.1 - - + +
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Residues in contact with MET 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PHE* 4.2 6.1 - - + -
106C ALA* 3.7 13.0 - - + -
108C ARG 4.5 0.2 - - - -
109C LYS* 3.4 7.4 - - - +
110C GLY 3.0 31.2 + - - +
112C TYR* 3.7 27.1 - - + -
114C PHE* 3.6 31.0 - - - -
133C LEU* 3.9 13.0 - - + -
159C ILE* 4.2 15.5 - - + -
160C GLN* 1.3 79.5 - - - +
162C GLU* 1.3 65.9 + - - +
165C ASP* 3.3 42.2 - - + +
167C ALA* 4.1 14.6 - - + -
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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