Contacts of the strand formed by residues 142 - 152 (chain G) in PDB entry 3HOX
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 ARG 142 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119D ARG* 5.4 2.0 - - - +
150D ASN* 3.2 47.9 + - - +
151D PHE* 3.9 39.3 - - + +
221D TYR* 5.9 1.2 - - - -
89G GLY 3.5 7.0 - - - +
90G THR* 4.4 5.6 - - + +
140G LYS 3.5 5.3 + - - +
141G SER* 1.3 75.6 - - - +
143G ILE* 1.3 67.0 + - - +
170G ALA* 3.7 5.0 - - - +
171G ILE* 3.4 41.0 + - + +
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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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88G ASP* 3.0 1.4 - - - -
89G GLY 2.9 31.1 + - - -
91G VAL* 3.3 26.7 - - + -
99G PHE* 3.4 20.9 - - + -
101G VAL* 4.1 8.6 - - + +
137G ILE* 3.4 25.4 - - + -
141G SER* 3.6 5.6 - - - +
142G ARG* 1.3 87.1 - - - +
144G ARG* 1.3 65.2 + - - +
145G VAL* 3.7 22.0 + - + +
163G ILE* 4.1 10.1 - - + -
169G GLY* 3.3 18.6 - - - +
170G ALA* 4.2 7.0 - - - -
171G ILE* 3.4 7.5 - - - +
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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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182D SER 4.7 1.0 + - - -
183D LEU* 3.0 28.1 - - - +
184D ALA* 3.1 42.0 + - - +
190D GLU* 4.2 5.5 + - - -
194D LEU* 3.4 27.5 - - - +
86G VAL* 3.9 9.4 - - + -
88G ASP* 2.7 38.7 + - + +
143G ILE* 1.3 71.4 - - - +
145G VAL* 1.3 59.1 + - - +
163G ILE* 3.7 5.0 - - - +
167G TYR 3.8 16.2 - - - +
168G LEU* 2.9 28.7 - - + +
169G GLY 2.8 27.0 + - - +
171G ILE* 3.6 12.4 - - + +
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Residues in contact with VAL 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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85G GLU 3.7 0.9 - - - +
86G VAL* 3.3 2.1 - - - +
87G VAL* 2.5 55.2 + - + +
101G VAL* 4.2 24.0 - - + -
108G VAL* 4.3 12.6 - - + -
110G VAL* 4.2 9.4 - - + -
143G ILE* 3.7 20.6 + - + +
144G ARG* 1.3 78.2 - - - +
146G LYS* 1.3 74.7 + - - +
147G ILE* 4.0 1.1 - - + +
161G GLY* 3.7 17.7 - - - -
162G SER 3.5 10.5 - - - +
163G ILE* 4.0 7.2 - - + -
168G LEU* 3.9 4.5 - - - -
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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
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84G GLY* 4.5 21.3 - - - -
85G GLU 3.7 3.1 - - - -
86G VAL* 4.3 14.6 - - + +
145G VAL* 1.3 76.2 - - - +
147G ILE* 1.3 63.1 + - - +
148G GLU* 3.1 31.0 + - - +
161G GLY* 3.0 1.9 - - - -
162G SER* 2.9 35.5 + - - +
165G GLU* 3.1 32.1 + - + -
168G LEU* 3.3 22.8 - - + +
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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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79G PHE* 6.5 0.2 - - + -
81G PRO* 4.5 9.4 - - + -
82G PHE 3.2 27.4 - - - +
83G LYS 3.4 0.2 - - - -
84G GLY* 2.5 34.2 + - - -
85G GLU* 2.9 35.1 + - + +
87G VAL* 3.8 28.3 - - + -
106G MET* 5.5 1.8 - - + -
108G VAL* 4.5 15.5 - - + -
145G VAL 5.2 0.2 - - - -
146G LYS* 1.3 69.8 - - - +
148G GLU* 1.3 59.6 + - - +
149G GLY 3.9 5.2 - - - +
150G CYS* 4.0 4.7 - - - -
159G ALA* 3.8 23.8 - - + -
160G ILE 3.7 11.4 - - - +
161G GLY* 4.0 2.2 - - - -
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Residues in contact with GLU 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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83G LYS* 3.3 25.3 - - - +
114G LEU* 3.8 22.6 - - + +
146G LYS* 3.1 33.6 + - - +
147G ILE* 1.3 72.1 - - - +
149G GLY* 1.3 54.8 + - - +
160G ILE* 2.6 18.5 + - + +
161G GLY* 4.1 0.2 - - - -
162G SER* 3.0 33.6 + - - +
165G GLU* 4.7 1.7 - - - +
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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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83G LYS* 4.7 8.5 - - - -
147G ILE* 3.5 2.5 - - - -
148G GLU* 1.3 80.5 - - - +
150G CYS* 1.3 64.1 + - - -
151G ILE* 4.9 2.1 - - - +
159G ALA* 3.0 4.2 - - - +
160G ILE* 2.7 38.7 + - - +
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Residues in contact with CYS 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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81G PRO* 4.0 25.6 - - + +
82G PHE* 4.0 18.8 - - - -
83G LYS* 4.6 1.2 - - - +
147G ILE* 4.0 12.1 - - - -
149G GLY* 1.3 72.8 - - - -
151G ILE* 1.3 64.9 + - - +
152G SER* 4.0 1.6 + - - +
157G ILE* 4.2 8.3 - - + -
158G HIS 3.5 7.0 - - - +
159G ALA* 3.6 17.0 - - - -
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Residues in contact with ILE 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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149G GLY 4.9 2.0 - - - +
150G CYS* 1.3 78.1 - - - +
152G SER* 1.3 71.8 + - - +
153G GLN* 3.4 19.7 + - - +
157G ILE* 4.5 1.1 - - - -
158G HIS* 2.7 63.2 + - + +
159G ALA* 4.6 0.9 - - - -
160G ILE* 4.6 18.8 - - + -
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Residues in contact with SER 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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40G GLY* 3.5 29.4 + - - -
80G LYS* 5.7 1.0 + - - -
150G CYS* 4.0 2.1 + - - +
151G ILE* 1.3 80.8 - - - +
153G GLN* 1.3 62.6 + - - +
156G SER 4.3 2.7 - - - -
157G ILE* 4.3 15.3 - - - +
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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