Contacts of the strand formed by residues 142 - 153 (chain G) in PDB entry 5IY8
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 142 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D ARG* 2.4 50.6 + - - +
71D PHE* 3.2 36.5 - - + -
86G ASP* 6.4 0.7 - - - -
87G ALA 3.4 4.7 - - - -
88G VAL* 4.6 2.7 - - + -
141G ASP* 1.3 75.2 - - - +
143G ILE* 1.3 58.5 + - - +
170G LEU* 3.1 33.9 - - + +
171G VAL* 4.0 6.9 + - + +
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Residues in contact with ILE 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D PHE* 5.6 0.2 - - - -
85G VAL 3.9 0.2 - - - +
86G ASP* 3.5 5.1 - - - +
87G ALA* 2.9 40.9 + - + +
89G VAL* 4.0 18.6 - - + -
97G LEU* 3.7 20.4 - - + -
99G THR* 3.6 30.5 - - + -
108G ILE* 3.7 11.4 - - + -
137G ILE* 4.1 17.7 - - + -
141G ASP* 4.1 5.4 - - + +
142G GLU* 1.3 78.9 - - - +
144G ARG* 1.3 65.0 - - - +
145G LEU* 4.0 0.8 + - + +
163G LEU* 4.3 10.1 - - + -
169G GLY* 3.3 13.2 - - - -
170G LEU* 3.9 10.3 - - + +
171G VAL* 6.2 0.2 - - - -
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Residues in contact with ARG 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ARG* 4.9 3.0 - - - +
103D LEU* 3.1 57.2 + - - +
104D CYS 4.9 2.2 + - - -
105D PRO 5.5 0.2 - - - -
110D GLU* 4.5 12.5 + - - -
114D LEU* 4.1 15.7 - - - +
84G VAL* 4.6 5.1 - - + +
85G VAL 3.5 5.8 - - - +
86G ASP* 3.2 33.1 + - - +
143G ILE* 1.3 72.9 - - - +
145G LEU* 1.3 60.8 + - - +
163G LEU* 3.5 6.6 - - - +
167G TYR 3.3 19.1 - - - +
168G LEU* 3.1 20.6 - - + +
169G GLY 2.7 40.7 + - - +
171G VAL* 3.4 35.8 - - + +
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Residues in contact with LEU 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G VAL* 3.4 2.9 - - - +
85G VAL* 2.9 53.7 + - + +
87G ALA* 3.7 16.2 - - + -
99G THR* 3.2 28.0 - - + +
101G ILE* 4.5 0.9 - - + -
106G CYS* 3.9 16.2 - - + -
108G ILE* 3.7 30.1 - - + -
143G ILE* 4.0 2.4 + - + -
144G ARG* 1.3 75.1 - - - +
146G LYS* 1.3 68.0 + - - +
147G ILE* 3.9 4.7 - - + +
161G GLY* 3.6 20.0 - - - -
162G SER 3.6 9.9 - - - +
163G LEU* 4.2 0.4 - - + -
168G LEU* 4.1 3.8 - - - -
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Residues in contact with LYS 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D SER* 5.3 9.0 - - - -
116D PRO* 6.3 1.2 - - - +
82G GLY* 3.5 32.8 - - - +
83G GLU 3.4 9.9 - - - +
84G VAL* 4.0 16.8 - - + +
145G LEU* 1.3 75.5 - - - +
147G ILE* 1.3 67.6 + - - +
148G VAL* 3.3 6.6 + - + +
161G GLY* 3.3 0.7 - - - -
162G SER* 2.9 36.0 + - - +
165G ASP* 3.2 27.7 + - + +
168G LEU* 4.2 13.2 - - + +
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Residues in contact with ILE 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G PHE* 5.9 0.4 - - + -
79G PRO* 3.7 27.1 - - + -
80G PHE 3.4 24.0 - - - +
81G LYS* 3.2 4.2 - - - +
82G GLY* 2.3 38.3 + - - -
83G GLU* 2.8 15.7 + - + +
85G VAL* 4.1 23.1 - - + -
104G MET* 5.0 5.8 - - + -
106G CYS* 5.2 1.3 - - - -
145G LEU* 3.9 16.6 - - + -
146G LYS* 1.3 69.4 - - - +
148G VAL* 1.3 57.9 + - - +
149G GLY 3.7 20.2 - - - +
150G THR* 4.6 2.9 - - + -
159G ALA* 4.4 14.4 - - + -
160G ILE 3.4 12.8 - - - +
161G GLY* 4.2 0.7 - - - -
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Residues in contact with VAL 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G LYS* 3.2 21.8 - - - +
82G GLY* 4.5 0.7 - - - +
146G LYS* 3.8 9.4 - - + +
147G ILE* 1.3 74.7 - - - +
149G GLY* 1.3 60.7 + - - +
160G ILE* 2.9 38.5 + - + +
161G GLY 4.7 3.6 - - - +
162G SER* 3.8 28.0 - - - -
138Q ASP* 5.1 1.3 - - - +
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Residues in contact with GLY 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G LYS* 4.1 9.6 - - - -
147G ILE* 3.5 4.0 - - - +
148G VAL* 1.3 84.1 - - - +
150G THR* 1.3 69.3 + - - +
159G ALA* 3.5 1.9 - - - +
160G ILE* 3.0 41.2 + - - +
139Q LEU* 6.1 0.2 - - - -
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Residues in contact with THR 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 5.3 1.0 + - - -
78G ARG* 3.8 34.6 + - - +
79G PRO* 4.1 14.8 - - + +
81G LYS* 5.3 4.6 - - + +
147G ILE* 4.6 7.0 - - + -
149G GLY* 1.3 79.3 - - - +
151G ARG* 1.3 64.3 + - - +
152G VAL* 5.9 0.6 - - - +
157G ILE* 4.6 8.1 - - + -
158G PHE 3.5 8.1 - - - +
159G ALA* 4.0 16.4 - - + +
160G ILE* 5.3 0.2 - - - -
139Q LEU* 4.7 8.1 - - - +
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Residues in contact with ARG 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G THR* 1.3 75.4 - - - +
152G VAL* 1.3 79.9 + - - +
153G ASP* 5.6 3.3 - - - +
157G ILE* 3.5 4.7 - - - +
158G PHE* 3.0 43.9 + - + -
137Q THR* 5.2 3.8 + - - +
139Q LEU* 3.4 43.3 - - + +
140Q GLU* 3.4 22.7 + - - -
143Q GLN* 6.2 0.2 - - - +
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Residues in contact with VAL 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134B THR* 5.6 4.0 - - - +
1143B LYS* 5.9 2.4 - - - -
40G GLY* 3.8 34.5 - - - +
78G ARG* 5.6 2.7 - - - +
150G THR* 5.9 0.4 - - - +
151G ARG* 1.3 90.7 + - - +
153G ASP* 1.3 60.9 + - - +
154G LYS 4.3 0.5 + - - -
155G ASN* 3.9 11.4 - - - +
156G ASP 3.3 22.0 - - - +
157G ILE* 3.7 22.7 - - + -
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Residues in contact with ASP 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133B HIS* 5.5 6.1 - - - -
1134B THR* 5.2 5.5 - - - +
151G ARG* 5.6 4.3 - - - +
152G VAL* 1.3 71.9 - - - +
154G LYS* 1.3 103.6 + - - +
155G ASN 3.1 0.9 - - - -
156G ASP* 2.8 27.5 + - - +
158G PHE* 3.7 19.0 - - + -
143Q GLN* 3.1 26.0 + - - +
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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