Contacts of the helix formed by residues 16 - 25 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.8 24.2 - - + -
8A HIS 3.1 36.1 - - - +
9A TYR* 3.5 27.1 - - + -
13A ARG 3.2 1.0 + - - -
15A ARG* 1.3 75.3 - - - +
17A GLU* 1.3 60.2 + - - +
18A SER 3.2 0.9 - - - -
19A VAL* 2.7 40.8 + - - +
20A ARG* 3.1 29.7 + - - +
56A PRO* 3.6 21.3 - - + +
57A MET 3.6 17.7 - - - +
58A VAL* 3.8 8.3 - - + -
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 2.9 38.5 + - + +
14A GLY 4.2 4.9 - - - +
15A ARG 3.1 1.0 - - - -
16A MET* 1.3 78.8 - - - +
18A SER* 1.3 58.8 + - - +
19A VAL 3.0 0.3 + - - -
20A ARG* 2.5 46.2 + - - +
21A TRP* 2.8 47.2 + - + +
162A GLN* 3.6 12.8 - - - +
197A PHE* 4.2 2.3 - - - -
204A LYS* 3.5 12.6 + - - +
205A LYS* 2.7 35.8 + - - +
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Residues in contact with SER 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG 3.8 10.6 + - - -
16A MET 3.2 0.8 - - - -
17A GLU* 1.3 78.9 - - - +
19A VAL* 1.3 64.3 + - - +
21A TRP* 3.4 3.2 - - - +
22A VAL* 3.0 26.9 + - - +
68A THR* 5.0 2.9 - - - +
72A LEU* 3.6 13.8 - - - +
100A LEU* 4.6 5.2 - - - +
103A LEU* 3.9 12.0 - - - +
159A ILE* 3.7 17.0 - - - +
162A GLN* 2.8 30.6 + - - +
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.6 3.4 - - + -
16A MET* 2.7 39.7 + - - +
18A SER* 1.3 78.7 - - - +
20A ARG* 1.3 66.4 + - - +
22A VAL* 3.1 3.5 + - - +
23A LEU* 2.8 34.7 + - + +
58A VAL* 4.7 5.8 - - + -
68A THR* 4.3 19.3 - - + -
71A ILE* 4.2 18.4 - - + -
72A LEU* 4.1 15.3 - - + -
75A ILE* 4.1 22.2 - - + -
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Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.0 8.7 - - + +
9A TYR* 4.2 3.4 - - - +
10A PRO 3.9 12.3 + - - -
12A GLY 2.7 27.5 + - - -
13A ARG 3.2 10.5 + - - -
16A MET* 3.7 23.4 - - - +
17A GLU* 2.5 45.7 + - - +
19A VAL* 1.3 75.7 - - - +
21A TRP* 1.3 65.0 + - - +
23A LEU* 3.7 0.5 - - - +
24A ALA* 2.8 26.9 + - - +
30A PHE* 3.8 28.4 - - + -
32A GLU* 2.8 27.2 + - - -
34A PHE* 4.1 2.6 - - - -
197A PHE* 4.1 15.3 - - + -
203A LYS 3.5 18.2 - - - -
205A LYS* 3.4 13.7 - - - +
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Residues in contact with TRP 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 2.8 35.3 + - + +
18A SER* 3.4 12.1 - - - +
20A ARG* 1.3 77.6 - - - +
22A VAL* 1.3 64.6 + - + +
24A ALA* 3.7 2.0 - - + +
25A ALA* 3.0 24.3 + - + +
158A VAL* 3.8 28.5 - - + +
159A ILE* 5.6 0.2 - - + -
161A LEU* 3.5 28.5 - - + -
162A GLN* 3.8 41.6 - - + +
165A LEU* 3.8 25.6 - - + -
194A ILE* 4.4 13.0 - - + -
197A PHE* 3.3 34.4 - + - -
198A LEU* 4.0 13.0 - - + -
204A LYS* 4.1 16.9 - - - +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER 3.0 16.2 + - - +
19A VAL* 3.8 2.5 - - - +
21A TRP* 1.3 77.4 - - - +
23A LEU* 1.3 65.7 + - - +
25A ALA* 3.2 2.7 + - - +
26A ALA* 2.9 20.8 + - - +
72A LEU* 3.9 11.9 - - + +
75A ILE* 3.8 23.6 - - + -
76A ALA 5.1 0.7 - - - +
81A LEU* 3.6 26.9 - - + -
155A LEU* 3.5 29.8 - - + -
158A VAL* 4.2 17.7 - - + -
159A ILE* 4.7 3.1 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.5 11.4 - - + -
7A LEU* 4.2 12.8 - - + -
19A VAL* 2.8 31.2 + - + +
22A VAL* 1.3 75.5 - - - +
24A ALA* 1.3 59.2 + - - +
26A ALA* 3.0 11.9 + - - +
27A GLY 3.1 0.2 + - - -
28A VAL* 2.9 53.1 + - + +
30A PHE* 3.4 45.3 - - + -
58A VAL* 5.5 2.0 - - + -
60A ILE* 5.9 2.5 - - + -
75A ILE* 3.8 32.3 - - + -
79A HIS* 5.6 1.3 - - + -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG 2.8 17.4 + - - +
21A TRP 3.7 3.6 - - - +
23A LEU* 1.3 75.1 - - - +
25A ALA* 1.3 60.5 + - - +
27A GLY* 2.7 20.1 + - - -
28A VAL 4.4 6.1 - - - +
30A PHE* 4.5 4.6 - - + -
193A THR* 3.3 13.4 - - - +
196A ARG* 5.3 0.5 + - - -
197A PHE* 3.3 39.9 - - + -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TRP* 3.0 17.9 + - + +
22A VAL 3.7 4.0 - - - +
24A ALA* 1.3 73.0 - - - +
26A ALA* 1.3 57.3 + - - +
27A GLY 2.8 9.1 + - - -
81A LEU* 5.4 3.1 - - + -
153A LEU* 4.6 13.5 - - + +
158A VAL* 4.3 24.0 - - + -
191A ILE* 5.6 0.5 - - - +
193A THR* 3.2 25.9 + - - +
194A 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