Contacts of the strand formed by residues 154 - 160 (chain A) in PDB entry 1K11
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 LEU 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A VAL* 4.8 9.0 - - + -
89A ILE* 3.9 30.1 - - + -
93A ASP* 5.6 4.0 - - - +
144A TYR* 2.8 68.5 + - + -
153A SER* 1.3 78.4 - - - +
155A LEU* 1.3 55.2 + - - +
156A ALA 4.1 1.1 + - - -
171A VAL* 4.8 0.4 - - + -
172A TYR 3.6 4.9 - - - +
173A GLN* 3.6 28.9 - - + +
176A SER* 2.8 10.6 + - - -
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Residues in contact with LEU 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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89A ILE* 5.1 0.2 - - - +
112A MET* 4.0 12.8 - - + -
141A MET* 3.6 35.4 - - + -
142A VAL 4.2 0.7 - - - -
143A CYS* 3.6 8.7 - - - -
153A SER 3.4 6.0 + - - +
154A LEU* 1.3 73.7 - - - +
156A ALA* 1.3 61.3 + - - +
157A LEU* 5.6 2.5 - - + -
171A VAL* 4.7 1.6 - - - -
172A TYR* 2.8 58.5 + - + +
176A SER* 3.3 24.7 - - - +
179A GLN* 3.5 37.7 - - + +
183A ILE* 5.2 0.9 - - + -
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Residues in contact with ALA 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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85A PRO* 3.5 31.9 - - + -
88A LEU* 3.9 15.3 - - + -
89A ILE* 4.5 10.7 - - + +
140A ARG 3.6 0.8 - - - +
141A MET* 3.2 8.3 - - - +
142A VAL 2.9 43.2 + - - +
154A LEU 4.1 0.8 - - - -
155A LEU* 1.3 72.7 - - - +
157A LEU* 1.3 60.2 + - - +
158A LYS* 4.2 1.6 - - + -
169A LEU* 6.0 0.2 - - + -
170A TRP 3.4 5.4 - - - -
171A VAL* 4.6 1.8 - - - +
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Residues in contact with LEU 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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88A LEU* 5.3 0.2 - - - +
112A MET* 5.0 1.8 - - - -
119A ILE* 3.9 22.2 - - + -
133A HIS* 4.4 8.7 - - - +
138A ILE* 3.8 45.8 - - + -
140A ARG 3.6 7.0 - - - +
141A MET* 4.1 18.6 - - + -
155A LEU* 3.8 2.7 + - + -
156A ALA* 1.3 74.6 - - - +
158A LYS* 1.3 60.7 + - - +
159A THR* 4.2 2.5 - - - +
169A LEU* 4.4 0.7 - - - -
170A TRP* 2.8 42.8 + - + +
172A TYR* 3.8 33.0 - - + +
183A ILE* 4.8 9.4 - - + -
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Residues in contact with LYS 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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73A LYS* 6.2 0.8 - - - +
75A LYS* 5.4 4.0 - - - +
76A LEU* 3.7 35.9 - - + +
80A LYS 4.3 2.4 + - - -
81A GLY* 3.8 13.3 - - - -
84A GLY* 4.5 3.2 - - - -
85A PRO* 3.5 33.2 - - + +
138A ILE* 3.5 4.3 - - - +
139A ILE* 2.9 41.0 + - + -
140A ARG* 2.9 45.8 + - + +
156A ALA* 5.7 0.9 - - + +
157A LEU* 1.3 70.1 - - - +
159A THR* 1.3 66.3 + - - +
167A TYR* 5.4 1.7 - - + -
168A SER 3.7 4.9 - - - -
169A LEU* 3.6 30.5 - - + +
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Residues in contact with THR 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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133A HIS* 4.0 27.3 - - + -
137A LEU* 3.3 29.2 - - + +
138A ILE* 3.3 15.0 - - + +
139A ILE* 4.1 1.6 - - - -
157A LEU* 4.0 1.4 + - - +
158A LYS* 1.3 77.7 + - - +
160A THR* 1.3 68.0 + - - +
161A ASP* 3.4 0.5 + - - -
168A SER* 2.8 38.3 + - - +
170A TRP* 3.4 26.2 - - + +
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Residues in contact with THR 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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137A LEU* 2.9 50.6 + - + +
139A ILE* 3.6 2.6 - - - +
159A THR* 1.3 75.4 - - - +
161A ASP* 1.3 61.1 + - - +
162A ALA* 3.5 21.3 - - + +
166A GLU 3.7 5.4 - - - +
167A TYR* 3.0 17.4 - - - -
795B TYR* 3.0 37.6 + - + +
796B GLU* 5.6 1.6 - - + +
797B GLY 4.8 10.8 - - - +
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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