Contacts of the strand formed by residues 151 - 161 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLU* 5.6 3.2 - - - +
118B VAL 3.5 1.4 - - - +
119B VAL* 3.5 4.3 - - - -
120B LYS* 3.0 37.1 + - + +
143B ALA* 4.2 14.9 - - + -
144B GLY* 3.6 36.8 + - - +
145B ASP 4.3 0.5 + - - -
146B GLN* 4.3 21.8 - - + +
149B THR* 4.1 5.4 + - + +
150B ARG* 1.3 78.7 - - - +
152B ALA* 1.3 62.7 + - - +
149C THR* 5.2 2.6 - - - +
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A SER 5.2 6.1 - - - +
117B HIS* 5.0 3.4 - - + -
118B VAL 3.3 11.7 - - - +
119B VAL* 4.6 11.4 - - + -
142B PHE 3.4 10.9 - - - +
143B ALA* 4.1 2.8 - - - +
151B GLU* 1.3 78.3 + - - +
153B ALA* 1.3 60.0 + - - +
154B SER* 3.4 20.3 + - - +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PHE* 3.4 12.3 - - - -
118B VAL* 3.0 29.3 + - - +
127B ILE* 4.5 3.8 - - + -
129B VAL* 3.9 23.1 - - + +
141B ALA* 3.5 20.4 - - + +
142B PHE* 3.4 23.8 - - - +
143B ALA* 3.9 6.1 - - + +
152B ALA* 1.3 70.3 - - - +
154B SER* 1.3 59.6 + - - +
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A SER* 5.0 3.0 + - - -
116B PHE 3.3 4.5 - - - -
117B HIS* 3.0 38.6 + - - -
141B ALA* 3.4 8.7 - - - +
142B PHE 4.7 0.2 + - - -
152B ALA* 3.4 22.8 + - - +
153B ALA* 1.3 75.4 - - - +
155B ASN* 1.3 66.1 + - - +
117C HIS* 3.5 18.3 + - - +
152C ALA* 5.4 4.7 - - - +
154C SER* 5.1 1.2 + - - -
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Residues in contact with ASN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASN* 3.7 3.1 - - - +
116B PHE* 3.2 46.2 + - + +
117B HIS* 5.5 1.1 + - - -
139B ILE* 3.9 17.6 - - + +
140B SER 3.0 25.9 + - - +
141B ALA* 4.9 0.2 - - - +
154B SER* 1.3 77.1 + - - +
156B GLY* 1.3 75.3 + - - +
117C HIS* 3.2 25.8 - - - +
119C VAL* 5.3 2.0 - - - +
182C TYR 3.9 6.1 + - - -
184C THR* 3.0 38.9 + - - +
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Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PHE 3.0 14.8 - - - -
115B ASN* 3.7 11.0 - - - -
116B PHE* 5.3 0.4 - - - -
139B ILE* 3.8 4.8 - - - +
155B ASN* 1.3 93.2 + - - +
157B VAL* 1.3 66.6 + - - +
115C ASN* 5.7 4.5 - - - +
117C HIS* 3.7 7.9 + - - -
184C THR* 3.7 10.6 + - - -
186C SER* 4.4 7.0 + - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B TYR 3.8 0.5 - - - +
113B SER* 3.6 2.7 + - - -
114B PHE* 3.0 30.9 + - - +
115B ASN* 5.5 0.2 - - - +
131B LEU* 3.7 20.6 - - + -
138B VAL* 4.6 0.7 - - + -
139B ILE* 3.5 38.6 - - + -
156B GLY* 1.3 75.7 - - - +
158B LEU* 1.3 77.9 + - - +
159B ILE* 4.0 13.4 + - + -
65C SER* 3.1 17.9 - - - +
67C ILE* 5.0 4.5 - - + -
90C LEU* 4.1 13.9 - - + -
184C THR* 5.5 3.4 - - - -
186C SER* 4.2 8.0 + - - -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ILE* 4.3 9.0 - - + -
112B TYR 3.4 3.8 - - - +
113B SER* 3.4 34.1 - - - +
157B VAL* 1.3 75.5 - - - +
159B ILE* 1.3 68.9 + - - +
190B VAL* 3.9 14.1 - - + -
63C ALA* 4.0 14.6 - - + -
64C PHE 3.5 11.2 - - - +
65C SER* 3.0 29.6 + - - +
90C LEU* 4.4 1.6 - - - +
91C VAL* 3.4 8.5 - - + +
186C SER* 4.2 7.1 - - - +
187C GLY 3.4 35.9 - - - +
188C PHE* 4.0 14.6 - - + -
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ILE* 4.4 2.2 - - - -
112B TYR* 2.9 28.3 + - - +
114B PHE* 3.7 36.1 - - + -
131B LEU* 4.6 11.0 - - + -
133B LEU* 4.3 21.5 - - + -
138B VAL* 3.8 32.5 - - + -
157B VAL* 4.0 9.2 - - + -
158B LEU* 1.3 80.8 - - - +
160B GLN* 1.3 63.1 + - - +
161B MET* 3.8 16.2 + - + -
167B ALA* 5.4 2.7 - - + -
90C LEU* 4.1 9.2 - - + -
91C VAL* 3.8 7.4 - - - -
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Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LYS* 4.6 3.3 - - + +
110B GLY 3.5 11.0 - - - +
111B ILE* 3.8 13.0 - - + +
133B LEU* 4.3 2.9 - - - +
159B ILE* 1.3 76.4 - - - +
161B MET* 1.3 72.2 + - - +
162B GLU* 3.4 10.5 + - - +
193B LEU* 3.5 25.1 - - + +
197B HIS* 4.9 3.6 + - - +
198B HIS 3.0 27.4 + - - +
199B HIS 3.6 0.2 - - - -
200B HIS* 3.1 52.7 + - + +
90C LEU 5.4 2.7 + - - +
91C VAL* 3.9 8.9 - - + +
93C ILE* 4.9 5.7 - - - +
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Residues in contact with MET 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PHE* 4.2 8.1 - - + -
106B ALA* 3.9 11.2 - - + -
108B ARG 4.0 0.8 - - - +
109B LYS* 3.3 8.8 - - - +
110B GLY 3.1 28.7 + - - -
112B TYR* 3.8 26.2 - - + -
114B PHE* 3.6 31.6 - - - -
133B LEU* 3.9 9.9 - - + -
159B ILE* 4.2 14.6 - - + -
160B GLN* 1.3 79.2 - - - +
162B GLU* 1.3 65.2 + - - +
165B ASP* 3.2 42.2 - - + +
167B ALA* 3.9 19.5 - - + +
200B HIS* 4.4 0.7 - - - -
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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