Contacts of the strand formed by residues 149 - 154 (chain M) in PDB entry 6K4Y
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 ILE 149 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142M LEU* 3.7 11.0 - - + +
144M LYS 3.8 0.5 - - - +
145M ARG* 3.3 22.2 - - - +
146M THR* 3.0 20.8 + - - +
147M ASN* 3.3 15.7 - - + +
148M GLY* 1.3 78.9 - - - +
150M ARG* 1.3 65.7 + - - +
151M ASN 4.2 0.2 - - - +
152M PHE* 3.6 35.7 - - + -
162M ILE* 3.8 11.7 - - + -
163M PHE 3.5 14.1 - - - +
164M GLY* 3.6 2.2 - - - -
167M MET* 3.7 20.2 - - + -
175M PHE* 4.9 4.5 - - + -
211M LEU* 3.7 29.8 - - + -
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Residues in contact with ARG 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141M ILE* 3.7 7.2 - - + +
142M LEU* 2.9 30.0 + - - +
144M LYS 5.0 0.3 - - - +
145M ARG* 4.7 8.3 - - + +
149M ILE* 1.3 75.3 - - - +
151M ASN* 1.3 67.5 + - - +
163M PHE* 2.9 40.7 + - - +
164M GLY* 3.4 5.1 - - - -
165M TYR* 3.3 33.5 - - + +
187M ASN* 5.7 0.2 - - - +
189M ASN* 2.9 33.5 + - - +
19N T 5.7 1.8 + - - -
41T T 3.4 30.9 + - - +
42T T 3.4 29.2 + - - +
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Residues in contact with ASN 151 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M LEU* 4.0 11.5 - - + +
140M ALA 3.8 1.1 - - - +
141M ILE* 3.7 31.4 - - + +
142M LEU 4.0 0.9 - - - +
149M ILE* 4.0 0.6 - - - +
150M ARG* 1.3 82.8 - - + +
152M PHE* 1.3 73.3 + - - +
153M GLU* 3.7 23.4 + - + +
162M ILE* 3.8 0.3 - - - +
163M PHE* 3.1 53.3 + - - +
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Residues in contact with PHE 152 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M MET* 3.8 9.3 - - - +
121M LEU* 3.6 38.8 - - + -
126M PHE* 5.2 6.1 - + + -
140M ALA* 2.8 44.6 + - + +
142M LEU* 3.6 32.8 - - + -
149M ILE* 3.6 31.0 - - + -
151M ASN* 1.3 79.1 - - - +
153M GLU* 1.3 60.6 + - - +
160M MET* 5.5 1.1 - - - -
161M ARG 3.6 1.1 - - - -
162M ILE* 3.6 33.0 - - + -
175M PHE* 6.0 0.2 - + - -
204M VAL* 6.2 1.3 - - + -
205M ILE* 5.6 3.1 - - + -
208M ALA* 4.3 24.5 - - + -
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Residues in contact with GLU 153 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M TYR 3.3 13.7 - - - +
139M LEU* 3.5 24.6 - - + +
140M ALA 4.2 1.8 - - - +
151M ASN* 3.7 16.1 + - - +
152M PHE* 1.3 76.0 - - - +
154M ILE* 1.3 62.1 + - - +
155M ASN* 4.4 11.7 + - - +
160M MET* 3.3 7.3 - - - +
161M ARG* 2.7 84.2 + - + +
163M PHE* 4.7 8.7 - - + +
191M TYR* 5.0 3.5 - - - -
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Residues in contact with ILE 154 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M MET* 3.3 17.3 - - + +
113M ASP* 4.3 16.2 - - + +
114M LYS* 4.3 9.4 - - - +
117M MET* 3.6 34.3 - - + -
137M ASN* 3.3 6.2 - - - +
138M TYR* 2.9 44.6 + - + +
153M GLU* 1.3 76.2 - - - +
155M ASN* 1.3 76.1 + - - +
159M ASN 4.8 1.6 - - - +
160M MET* 3.7 22.7 - - + +
196M ARG* 3.6 28.7 - - + +
201M ILE* 6.2 1.1 - - + -
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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