Contacts of the strand formed by residues 156 - 166 (chain G) in PDB entry 3GUT
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 ALA 156 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34G PHE* 4.1 3.2 - - - -
79G LYS* 4.7 15.1 + - + +
86G HIS* 3.3 13.5 + - - -
153G ASP* 3.5 19.4 + - - +
154G LEU 3.4 2.0 + - - -
155G ASN* 1.3 82.3 - - - +
157G VAL* 1.3 74.2 + - - +
182G PRO* 4.9 1.8 - - + -
183G ILE 2.8 18.2 - - - +
184G PHE* 3.4 22.9 - - + +
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Residues in contact with VAL 157 (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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34G PHE* 4.6 9.0 - - + -
76G LEU* 4.0 28.7 - - + -
77G VAL 3.6 9.2 - - - +
79G LYS* 4.8 5.2 - - - +
86G HIS* 3.3 38.6 - - + +
88G HIS* 4.5 7.9 - - + -
118G ILE* 4.6 6.7 - - + -
156G ALA* 1.3 87.4 - - - +
158G ARG* 1.3 67.1 + - - +
159G LEU* 5.6 0.2 - - + -
182G PRO* 3.0 7.2 - - - +
183G ILE* 2.6 50.1 + - + +
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Residues in contact with ARG 158 (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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75G SER 3.4 2.4 - - - +
76G LEU* 3.5 5.9 - - - +
77G VAL* 3.2 37.7 + - + +
78G THR 3.8 6.5 - - - +
79G LYS* 2.5 34.9 + - - +
80G ASP* 5.4 1.0 + - - -
83G HIS* 4.2 3.2 - - - -
157G VAL* 1.3 82.5 - - - +
159G LEU* 1.3 67.5 + - - +
160G CYS 3.7 0.2 + - - -
179G LEU* 3.4 33.5 - - + +
180G SER* 3.0 38.1 + - - +
181G HIS* 3.3 12.3 - - - +
182G PRO* 3.4 26.2 - - + +
183G ILE* 5.1 1.3 - - - -
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Residues in contact with LEU 159 (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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27G PRO* 3.7 33.0 - - + -
46G ILE* 5.3 3.8 - - + -
59G PRO* 4.7 4.5 - - + -
74G ILE* 4.1 14.1 - - + -
75G SER 3.5 1.6 - - - -
76G LEU* 3.8 23.1 - - + -
90G LEU* 4.1 13.7 - - + -
116G LEU* 4.6 17.5 - - + -
118G ILE* 4.9 7.0 - - + -
157G VAL* 5.6 0.2 - - + -
158G ARG* 1.3 75.4 - - - +
160G CYS* 1.3 59.3 - - - +
161G PHE* 4.0 27.6 - - + -
178G VAL 3.6 0.7 - - - +
179G LEU* 3.4 6.4 - - - +
180G SER* 2.7 35.7 + - - +
183G ILE* 4.9 9.6 - - + -
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Residues in contact with CYS 160 (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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73G ARG 3.3 1.4 - - - +
74G ILE* 3.6 0.8 - - - -
75G SER 2.6 41.2 + - - +
77G VAL* 4.1 13.7 - - + -
140G PRO* 4.0 16.6 - - + -
141G PHE* 4.0 3.6 - - - -
159G LEU* 1.3 75.1 - - - +
161G PHE* 1.3 60.3 + - - +
162G GLN* 3.2 14.2 + - - +
177G PRO* 3.7 29.4 - - - -
178G VAL 3.3 4.5 - - - -
179G LEU* 3.5 25.1 - - + -
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Residues in contact with PHE 161 (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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23G ILE* 4.1 22.9 - - + -
27G PRO* 5.6 0.9 - - + -
59G PRO* 4.8 11.7 - - + -
61G ILE* 3.7 29.2 - - + -
72G VAL* 5.0 0.2 - - + -
73G ARG 3.8 2.5 - - - -
74G ILE* 2.7 39.7 - - + -
113G PHE* 4.1 18.2 - + - -
116G LEU* 5.5 1.1 - - + -
159G LEU* 4.0 34.3 - - + -
160G CYS* 1.3 70.8 - - - +
162G GLN* 1.3 62.2 + - - +
163G VAL* 3.8 13.2 + - + +
176G THR 4.2 1.6 - - - +
177G PRO* 3.4 3.1 - - - +
178G VAL* 2.9 54.7 + - + +
179G LEU 5.2 0.2 - - - -
180G SER* 4.4 6.7 - - - -
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Residues in contact with GLN 162 (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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71G THR 4.1 0.3 - - - +
72G VAL* 3.5 2.5 - - - +
73G ARG* 2.9 64.1 + - + +
75G SER* 3.1 34.6 - - - -
138G ASN* 4.7 0.9 + - - +
140G PRO* 3.8 32.9 - - + +
160G CYS* 3.2 15.9 + - - +
161G PHE* 1.3 74.3 - - - +
163G VAL* 1.3 62.2 + - - +
164G THR* 4.7 2.1 + - - -
174G LEU* 4.8 13.9 - - + -
175G LEU 5.8 0.4 - - - -
176G THR 5.6 0.2 - - - -
177G PRO* 4.2 12.3 - - + -
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Residues in contact with VAL 163 (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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21G VAL* 3.2 42.6 - - + -
61G ILE* 4.2 8.1 - - + -
63G ILE* 3.7 14.1 - - + -
71G THR 3.6 2.5 - - - -
72G VAL* 4.2 13.9 - - + +
104G LEU* 3.5 28.7 - - + -
161G PHE 3.8 7.1 + - - +
162G GLN* 1.3 73.7 - - - +
164G THR* 1.3 65.7 + - - +
165G VAL* 4.0 5.8 - - + -
174G LEU* 3.6 3.3 - - - +
175G LEU* 3.1 35.4 + - + +
176G THR 5.3 1.8 + - - -
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Residues in contact with THR 164 (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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70G GLY* 3.3 5.2 - - - -
71G THR* 2.6 48.4 + - - +
104G LEU* 5.1 0.2 - - - -
162G GLN 4.7 1.9 + - - -
163G VAL* 1.3 71.1 - - - +
165G VAL* 1.3 70.7 + - - +
166G ARG* 5.3 1.5 + - - +
172G PRO* 4.4 11.7 - - + -
173G LEU 3.4 17.7 - - - +
174G LEU* 3.0 26.6 - - + +
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Residues in contact with VAL 165 (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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19G ALA* 4.9 2.0 - - + -
63G ILE* 4.3 12.8 - - + -
66G TYR* 3.3 51.1 - - + -
69G PRO 4.1 4.3 - - - -
70G GLY* 4.6 0.4 - - - -
104G LEU* 4.8 3.6 - - + -
163G VAL* 4.0 17.0 - - + -
164G THR* 1.3 78.0 - - - +
166G ARG* 1.3 66.0 + - - +
172G PRO* 3.5 2.6 - - - +
173G LEU* 2.6 52.3 + - + +
175G LEU* 3.7 24.2 - - + -
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Residues in contact with ARG 166 (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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66G TYR* 3.0 35.4 - - + +
69G PRO* 3.7 35.5 - - - +
70G GLY* 4.5 6.4 - - - +
164G THR* 5.3 1.6 + - - +
165G VAL* 1.3 83.9 + - - +
167G ASP* 1.3 70.5 + - - +
170G GLY* 3.5 24.5 - - - +
171G ARG* 3.7 10.7 - - - +
172G PRO* 3.7 26.6 - - + +
173G LEU* 3.8 4.3 - - - +
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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