Contacts of the helix formed by residues 16 - 25 (chain G) in PDB entry 1GUM
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 MET 16 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G LEU* 3.8 24.9 - - + -
8G HIS 3.1 35.7 - - - +
9G TYR* 3.5 26.3 - - + -
13G ARG 3.2 0.8 + - - -
15G ARG* 1.3 76.2 - - - +
17G GLU* 1.3 59.0 + - - +
18G SER 3.2 1.1 - - - -
19G VAL* 2.7 40.3 + - - +
20G ARG* 3.1 28.6 + - - +
56G PRO* 3.6 21.7 - - + +
57G MET 3.6 17.5 - - - +
58G VAL* 3.8 8.7 - - + -
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Residues in contact with GLU 17 (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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13G ARG* 2.9 39.4 + - + +
14G GLY 4.2 5.4 - - - +
15G ARG 3.1 1.2 - - - -
16G MET* 1.3 77.3 - - - +
18G SER* 1.3 58.9 + - - +
19G VAL 3.0 0.3 + - - -
20G ARG* 2.5 44.7 + - - +
21G TRP* 2.8 45.8 + - + +
162G GLN* 3.6 11.9 - - - +
197G PHE* 4.2 2.6 - - - -
204G LYS* 3.5 13.3 + - - +
205G LYS* 2.7 35.4 + - - +
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Residues in contact with SER 18 (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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15G ARG 3.8 10.8 + - - -
16G MET 3.2 0.4 - - - -
17G GLU* 1.3 78.6 - - - +
19G VAL* 1.3 64.0 + - - +
21G TRP* 3.4 3.7 - - - +
22G VAL* 3.0 27.0 + - - +
68G THR* 5.0 2.8 - - - +
72G LEU* 3.9 12.9 - - - +
100G LEU* 4.6 5.6 - - - +
103G LEU* 3.9 12.0 - - - +
159G ILE* 3.7 17.0 - - - +
162G GLN* 2.8 30.2 + - - +
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Residues in contact with VAL 19 (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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7G LEU* 4.6 2.5 - - + -
16G MET* 2.7 39.7 + - - +
18G SER* 1.3 78.9 - - - +
20G ARG* 1.3 64.6 - - - +
22G VAL* 3.1 3.5 + - - +
23G LEU* 2.8 35.7 + - + +
56G PRO* 5.5 0.4 - - + -
58G VAL* 4.7 6.3 - - + -
68G THR* 4.3 18.8 - - + -
71G ILE* 4.2 17.5 - - + -
72G LEU* 4.1 16.2 - - + -
75G ILE* 4.1 22.4 - - + -
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Residues in contact with ARG 20 (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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7G LEU* 4.0 8.9 - - + +
9G TYR* 4.2 3.4 - - - +
10G PRO 3.9 12.1 + - - -
12G GLY 2.7 27.1 + - - -
13G ARG 3.2 10.3 + - - -
16G MET* 3.7 23.4 - - - +
17G GLU* 2.5 45.6 + - - +
19G VAL* 1.3 74.3 - - - +
21G TRP* 1.3 65.3 + - - +
23G LEU* 3.7 0.5 - - - +
24G ALA* 2.8 27.2 + - - +
30G PHE* 3.8 29.0 - - + -
32G GLU* 2.8 27.0 + - - -
34G PHE* 4.1 2.6 - - - -
197G PHE* 4.1 15.3 - - + -
203G LYS 3.5 18.2 - - - -
205G LYS* 3.4 14.5 - - - +
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Residues in contact with TRP 21 (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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17G GLU* 2.8 36.1 + - + +
18G SER* 3.4 12.6 - - - +
20G ARG* 1.3 77.6 - - - +
22G VAL* 1.3 65.3 + - + +
24G ALA* 3.7 2.0 - - + +
25G ALA* 3.0 23.8 + - + +
158G VAL* 3.8 28.5 - - + +
159G ILE* 5.6 0.2 - - + -
161G LEU* 3.5 28.3 - - + -
162G GLN* 3.8 40.3 - - + +
165G LEU* 3.8 25.8 - - + -
194G ILE* 4.4 13.9 - - + -
197G PHE* 3.3 34.2 - + + -
198G LEU* 4.0 12.6 - - + -
204G LYS* 4.1 17.1 - - - +
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Residues in contact with VAL 22 (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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18G SER 3.0 16.2 + - - +
19G VAL 3.1 2.9 + - - +
21G TRP* 1.3 78.3 - - - +
23G LEU* 1.3 65.3 + - - +
25G ALA* 3.2 2.6 + - - +
26G ALA* 2.9 20.6 + - - +
72G LEU* 3.9 12.3 - - + -
75G ILE* 3.8 23.3 - - + -
76G ALA 5.1 0.4 - - - +
81G LEU* 3.6 27.1 - - + -
155G LEU* 3.5 29.4 - - + -
158G VAL* 4.2 17.9 - - + -
159G ILE* 4.7 3.4 - - + -
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Residues in contact with LEU 23 (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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5G PRO* 4.5 11.0 - - + -
7G LEU* 4.2 13.0 - - + -
19G VAL* 2.8 30.9 + - + +
20G ARG 3.7 0.2 - - - +
22G VAL* 1.3 75.8 - - - +
24G ALA* 1.3 58.6 - - - +
26G ALA* 3.0 11.6 + - - +
28G VAL* 2.8 54.4 + - + +
30G PHE* 3.4 43.5 - - + -
58G VAL* 5.5 2.2 - - + -
60G ILE* 5.9 2.7 - - + -
75G ILE* 3.8 32.5 - - + -
79G HIS* 5.6 1.6 - - + -
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Residues in contact with ALA 24 (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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20G ARG 2.8 18.1 + - - +
21G TRP 3.7 3.6 - - - +
23G LEU* 1.3 74.5 - - - +
25G ALA* 1.3 61.5 + - - +
27G GLY* 2.7 20.5 + - - +
28G VAL 4.1 6.3 + - - +
30G PHE* 4.5 4.7 - - + -
193G THR* 3.3 13.7 - - - +
194G ILE* 6.0 0.2 - - - -
196G ARG* 5.3 0.2 + - - -
197G PHE* 3.3 38.6 - - + -
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Residues in contact with ALA 25 (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 TRP* 3.0 18.7 + - + +
22G VAL 3.7 3.6 - - - +
24G ALA* 1.3 73.2 - - - +
26G ALA* 1.3 58.9 - - - +
27G GLY 2.8 8.7 + - - -
81G LEU* 5.4 2.9 - - + -
153G LEU* 4.6 14.6 - - + +
158G VAL* 4.3 23.8 - - + -
191G ILE* 5.6 0.3 - - - +
193G THR* 3.2 25.7 + - - +
194G ILE* 4.3 19.7 - - + +
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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