Contacts of the strand formed by residues 151 - 161 (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 GLU 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A VAL 3.9 0.5 - - - +
119A VAL* 3.7 3.3 - - - -
120A LYS* 3.2 34.8 + - + +
143A ALA* 4.2 10.2 - - + +
144A GLY* 2.7 43.6 + - - +
146A GLN* 2.4 34.7 + - - +
149A THR* 4.0 3.1 + - + +
150A ARG* 1.3 74.4 - - - +
152A ALA* 1.3 60.7 + - - +
153A ALA 4.3 0.2 + - - -
149B THR* 5.3 1.9 - - - +
151B GLU* 5.6 2.8 - - - +
142C PHE 5.9 0.4 - - - -
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Residues in contact with ALA 152 (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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117A HIS* 4.6 8.3 - - + +
118A VAL 3.3 9.9 - - - +
119A VAL* 4.0 18.2 - - + -
142A PHE 3.9 6.1 - - - +
143A ALA* 4.3 4.5 - - - +
151A GLU* 1.3 77.5 - - - +
153A ALA* 1.3 59.3 + - - +
154A SER* 3.5 21.6 + - - +
154C SER 5.3 4.7 - - - +
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Residues in contact with ALA 153 (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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116A PHE* 3.4 12.6 - - - -
118A VAL* 2.9 31.4 + - - +
127A ILE* 4.3 4.5 - - + -
129A VAL* 4.1 18.4 - - + -
141A ALA* 3.5 22.0 - - + +
142A PHE 3.5 25.1 - - - +
143A ALA* 4.1 7.8 - - + +
152A ALA* 1.3 70.4 - - - +
154A SER* 1.3 57.9 + - - +
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Residues in contact with SER 154 (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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116A PHE 3.3 4.5 - - - -
117A HIS* 2.9 38.3 + - - -
141A ALA* 3.4 9.9 - - - +
142A PHE 4.9 0.6 + - - -
152A ALA* 3.5 19.5 + - - +
153A ALA* 1.3 75.9 - - - +
155A ASN* 1.3 66.9 + - - +
117B HIS* 3.5 18.7 + - - +
152B ALA* 5.2 6.1 - - - +
154B SER* 5.0 3.1 + - - -
154C SER* 5.9 0.7 - - - -
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Residues in contact with ASN 155 (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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115A ASN* 3.7 2.5 - - - +
116A PHE* 3.1 50.5 + - + +
117A HIS* 5.6 0.5 + - - -
139A ILE* 3.9 12.8 - - + +
140A SER 3.0 25.0 + - - +
141A ALA* 5.0 0.2 - - - +
154A SER* 1.3 77.7 + - - +
156A GLY* 1.3 76.4 + - - +
117B HIS* 3.3 23.1 - - - +
119B VAL* 4.9 3.0 - - - +
182B TYR 3.5 8.7 + - - -
184B THR* 2.8 41.1 + - - +
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Residues in contact with GLY 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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114A PHE 3.1 15.0 - - - -
115A ASN* 3.8 10.1 - - - -
116A PHE* 5.3 0.2 - - - -
139A ILE* 3.6 7.2 - - - +
155A ASN* 1.3 93.1 + - - +
157A VAL* 1.3 65.6 + - - +
115B ASN* 6.0 2.6 - - - +
117B HIS* 3.7 7.6 + - - -
184B THR* 3.6 12.3 + - - -
186B SER* 4.6 6.4 + - - -
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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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112A TYR 3.9 0.5 - - - +
113A SER* 3.7 1.7 + - - -
114A PHE* 3.0 33.0 + - + +
115A ASN* 5.0 0.2 + - - -
131A LEU* 3.8 19.7 - - + -
138A VAL* 4.3 2.0 - - + -
139A ILE* 3.6 31.2 - - + -
156A GLY* 1.3 74.4 - - - +
158A LEU* 1.3 78.2 + - - +
159A ILE* 3.9 14.0 + - + -
65B SER* 3.1 16.6 - - - +
66B ALA 5.8 0.2 - - - +
67B ILE* 4.7 5.4 - - + -
90B LEU* 3.7 20.9 - - + -
184B THR* 5.4 2.0 - - + -
186B SER* 4.4 6.9 + - - -
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Residues in contact with LEU 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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111A ILE* 4.3 9.2 - - + -
112A TYR 3.3 4.5 - - - +
113A SER* 3.4 35.4 - - - +
157A VAL* 1.3 78.1 - - - +
159A ILE* 1.3 66.2 + - - +
190A VAL* 4.0 12.6 - - + -
63B ALA* 4.2 13.5 - - + -
64B PHE 3.4 21.8 - - - +
65B SER* 3.1 27.4 + - - +
90B LEU* 4.1 1.0 - - - +
91B VAL* 3.2 8.7 - - + +
186B SER* 4.1 7.6 - - - +
187B GLY 3.5 21.1 - - - +
188B PHE* 3.9 20.2 - - + -
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Residues in contact with ILE 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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111A ILE* 3.6 1.7 - - - -
112A TYR* 2.9 28.5 + - - +
114A PHE* 3.8 34.5 - - + -
131A LEU* 4.8 10.5 - - + -
133A LEU* 4.2 23.1 - - + -
138A VAL* 3.8 29.2 - - + -
157A VAL* 3.9 8.1 - - + -
158A LEU* 1.3 81.7 - - - +
160A GLN* 1.3 63.2 + - - +
161A MET* 3.7 16.8 + - + -
167A ALA* 5.6 2.5 - - + -
90B LEU* 4.0 11.4 - - + -
91B VAL* 3.7 7.9 - - - -
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Residues in contact with GLN 160 (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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109A LYS* 4.2 15.4 - - + +
110A GLY 3.5 11.4 - - - +
111A ILE* 3.6 13.2 - - + +
133A LEU* 4.5 8.8 - - - +
159A ILE* 1.3 76.6 - - - +
161A MET* 1.3 69.6 + - - +
162A GLU* 3.5 21.8 + - - +
165A ASP* 4.9 0.3 - - - +
193A LEU* 3.5 25.9 - - + +
90B LEU 5.1 4.1 + - - +
91B VAL* 3.9 8.1 - - + +
93B ILE* 4.9 5.4 - - - +
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Residues in contact with MET 161 (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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104A PHE* 4.4 4.0 - - + +
106A ALA* 3.9 12.8 - - + -
108A ARG 3.8 0.7 - - - +
109A LYS* 3.2 5.5 - - - +
110A GLY 3.0 31.6 + - - +
112A TYR* 3.7 24.0 - - + -
114A PHE* 3.6 32.8 - - - -
133A LEU* 3.7 15.7 - - + -
159A ILE* 3.7 16.4 + - + -
160A GLN* 1.3 80.1 - - - +
162A GLU* 1.3 63.7 + - - +
165A ASP* 3.4 42.6 - - + +
167A ALA* 4.1 14.1 - - + -
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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