Contacts of the strand formed by residues 149 - 157 (chain Z) in PDB entry 6F0X
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 CYS 149 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36Z GLY 5.5 0.8 + - - -
37Z ILE* 3.6 33.8 + - + +
38Z TYR* 5.1 2.3 - - - -
88Z ILE* 3.8 16.4 - - + -
89Z SER 3.1 15.5 - - - +
90Z ASN* 4.6 0.7 - - - -
91Z ILE* 3.9 9.3 - - - +
97Z LEU* 3.6 31.2 - - - -
145Z LEU* 3.8 21.9 - - + +
147Z VAL* 4.1 7.9 - - - -
148Z SER* 1.3 83.0 - - - +
150Z SER* 1.3 61.2 + - - +
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Residues in contact with SER 150 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Z ILE* 4.7 1.6 - - - -
38Z TYR* 5.5 5.6 - - - -
88Z ILE* 3.4 6.1 - - - +
89Z SER* 2.6 37.5 + - - +
90Z ASN 3.3 18.7 + - - -
91Z ILE* 4.3 10.3 + - - -
149Z CYS* 1.3 74.2 - - - +
151Z PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 151 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Q GLY* 4.9 17.6 - - - -
28Z ILE* 5.8 0.2 - - + -
32Z LEU* 3.6 24.9 - - + -
37Z ILE* 3.8 16.4 - - + -
38Z TYR* 3.0 44.2 + + - -
61Z LEU* 4.0 16.6 - - + -
64Z TYR* 5.9 0.2 - + - -
65Z LEU* 5.9 0.4 - - + -
86Z VAL* 3.9 7.6 - - + -
87Z VAL 3.2 12.8 - - - +
88Z ILE* 3.6 18.2 - - + -
89Z SER* 4.3 1.8 - - - +
150Z SER* 1.3 81.3 + - - +
152Z ASP* 1.3 65.0 + - - +
153Z LEU* 3.7 37.9 - - + -
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Residues in contact with ASP 152 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132Q ARG* 3.0 49.3 + - - +
133Q LEU 4.1 14.9 + - - +
135Q GLY* 5.4 3.7 + - - -
64Z TYR* 5.4 0.7 + - - -
86Z VAL 3.7 0.2 - - - -
87Z VAL* 2.7 41.4 + - + +
151Z PHE* 1.3 76.7 - - - +
153Z LEU* 1.3 87.4 + - - +
154Z LEU* 5.3 2.0 - - + -
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Residues in contact with LEU 153 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Q LEU 3.2 17.2 - - - +
132Q ARG* 4.0 8.3 - - - +
133Q LEU 5.0 0.3 + - - -
28Z ILE* 5.6 6.7 - - + -
64Z TYR* 3.3 41.3 - - + +
65Z LEU* 4.0 16.4 - - + -
68Z VAL* 4.9 8.3 - - + -
84Z LEU* 6.1 3.1 - - + -
85Z VAL 3.9 2.5 - - - +
86Z VAL* 3.5 42.6 - - + -
151Z PHE* 3.7 22.0 - - + -
152Z ASP* 1.3 85.0 + - - +
154Z LEU* 1.3 62.1 + - - +
155Z ILE* 5.4 3.3 - - + +
167Z TRP* 5.1 5.3 - - + -
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Residues in contact with LEU 154 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q ILE* 3.5 24.9 - - + -
131Q LEU 4.2 0.9 - - - +
132Q ARG* 3.1 39.7 - - + +
85Z VAL* 2.7 54.5 + - + +
87Z VAL* 3.6 27.1 - - + -
99Z ARG* 5.0 3.8 - - - +
152Z ASP* 3.9 2.8 + - - +
153Z LEU* 1.3 73.4 - - - +
155Z ILE* 1.3 65.9 + - - +
171Z GLY 3.9 2.5 - - - +
172Z PRO 3.5 24.7 - - - +
173Z GLN* 3.8 11.4 - - + -
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Residues in contact with ILE 155 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129Q LYS 2.8 34.9 - - - +
130Q ILE* 3.2 15.4 - - - +
131Q LEU* 4.2 19.5 + - + +
68Z VAL* 6.2 2.9 - - + -
72Z LEU* 5.0 9.2 - - + -
75Z TRP* 4.0 25.1 - - + -
81Z VAL* 3.7 12.6 - - + -
83Z LYS* 3.3 16.2 - - - +
84Z LEU* 3.4 26.9 - - + +
85Z VAL* 5.6 0.9 - - - -
153Z LEU* 5.4 3.1 - - + -
154Z LEU* 1.3 81.3 - - - +
156Z TYR* 1.3 69.5 - - - +
157Z THR* 3.4 15.0 - - + +
167Z TRP* 5.8 6.3 - - + -
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Residues in contact with TYR 156 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Q LYS* 3.4 53.7 + - + -
130Q ILE* 4.3 10.5 - - + -
81Z VAL* 3.5 3.4 - - - -
82Z GLN* 2.8 37.5 + - + +
83Z LYS* 3.1 41.6 + - + -
155Z ILE* 1.3 79.6 - - - +
157Z THR* 1.3 56.8 + - - +
158Z ASP* 4.2 17.5 - - + +
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Residues in contact with THR 157 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Q LYS* 3.0 31.6 + - - +
131Q LEU* 3.9 15.0 - - + -
75Z TRP* 4.3 12.5 - - + -
80Z SER* 2.6 35.1 + - - -
81Z VAL* 3.6 12.3 - - - +
155Z ILE* 3.4 8.6 - - + +
156Z TYR* 1.3 72.9 - - - +
158Z ASP* 1.3 68.2 + - - +
159Z LYS* 3.0 21.0 + - - +
162Z VAL* 5.0 4.7 - - + +
163Z VAL* 5.6 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