Contacts of the helix formed by residues 16 - 25 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E LEU* 3.8 24.9 - - + -
8E HIS 3.1 35.2 - - - +
9E TYR* 3.5 26.5 - - + -
13E ARG 3.2 1.4 + - - -
15E ARG* 1.3 75.9 - - - +
17E GLU* 1.3 58.9 + - - +
18E SER 3.2 1.3 - - - -
19E VAL* 2.7 40.6 + - - +
20E ARG* 3.1 30.5 + - - +
56E PRO* 3.6 23.0 - - + +
57E MET 3.6 17.0 - - - +
58E VAL* 3.8 9.2 - - + -
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Residues in contact with GLU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ARG* 2.9 39.3 + - + +
14E GLY 4.2 5.4 - - - +
15E ARG 3.1 0.8 - - - -
16E MET* 1.3 78.1 - - - +
18E SER* 1.3 58.3 + - - +
19E VAL 3.0 0.3 + - - -
20E ARG* 2.5 45.6 + - - +
21E TRP* 2.8 45.9 + - + +
162E GLN* 3.6 12.6 - - - +
197E PHE* 4.2 2.4 - - - -
204E LYS* 3.5 13.6 + - - +
205E LYS* 2.7 35.0 + - - +
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Residues in contact with SER 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ARG* 3.8 11.4 + - - -
16E MET 3.2 1.0 - - - -
17E GLU* 1.3 78.9 - - - +
19E VAL* 1.3 63.4 + - - +
21E TRP* 3.4 3.8 - - - +
22E VAL* 3.0 27.0 + - - +
68E THR* 5.0 3.5 - - - +
72E LEU* 3.6 14.1 - - - +
100E LEU* 4.6 5.0 - - - +
103E LEU* 3.9 11.4 - - - +
159E ILE* 3.7 16.9 - - - +
162E GLN* 2.8 31.0 + - - +
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Residues in contact with VAL 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU* 4.6 3.1 - - + -
16E MET* 2.7 39.9 + - - +
18E SER* 1.3 77.2 - - - +
20E ARG* 1.3 65.0 + - - +
22E VAL* 3.1 3.3 + - - +
23E LEU* 2.8 35.3 + - + +
56E PRO* 5.5 0.2 - - + -
58E VAL* 4.7 6.1 - - + -
68E THR* 4.3 18.8 - - + -
71E ILE* 4.2 18.4 - - + -
72E LEU* 4.1 15.7 - - + -
75E ILE* 4.1 22.4 - - + -
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Residues in contact with ARG 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU* 4.0 8.5 - - + +
9E TYR* 4.2 3.2 - - - +
10E PRO 3.9 12.3 + - - -
12E GLY 2.7 27.8 + - - -
13E ARG 3.2 9.9 + - - -
16E MET* 3.7 23.6 - - - +
17E GLU* 2.5 45.7 + - - +
19E VAL* 1.3 76.3 - - - +
21E TRP* 1.3 64.7 + - - +
23E LEU* 3.7 0.5 - - - +
24E ALA* 2.8 27.2 + - - +
30E PHE* 3.8 28.6 - - + -
32E GLU* 2.8 27.8 + - - -
34E PHE* 4.1 2.6 - - - -
197E PHE* 4.1 14.8 - - + -
203E LYS 3.5 17.9 - - - -
205E LYS* 3.4 14.3 - - - +
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Residues in contact with TRP 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E GLU* 2.8 34.9 + - + +
18E SER* 3.4 12.3 - - - +
20E ARG* 1.3 77.7 - - - +
22E VAL* 1.3 64.7 + - - +
24E ALA* 3.7 1.8 - - - +
25E ALA* 3.0 23.8 + - + +
158E VAL* 3.8 29.3 - - + +
159E ILE* 5.6 0.4 - - + -
161E LEU* 3.5 26.5 - - + -
162E GLN* 3.8 41.7 - - + +
165E LEU* 3.8 25.6 - - + -
194E ILE* 4.4 14.4 - - + -
197E PHE* 3.3 35.0 - + - -
198E LEU* 4.0 12.6 - - + -
204E LYS* 4.1 17.9 - - - +
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E SER 3.0 16.9 + - - +
19E VAL 3.8 2.7 - - - +
21E TRP* 1.3 76.5 - - - +
23E LEU* 1.3 65.2 + - - +
25E ALA* 3.2 3.0 + - - +
26E ALA* 2.9 20.8 + - - +
72E LEU* 3.9 11.4 - - + -
75E ILE* 3.8 24.5 - - + -
76E ALA 5.1 0.4 - - - +
81E LEU* 3.6 26.7 - - + -
155E LEU* 3.5 30.7 - - + -
158E VAL* 4.2 17.5 - - + -
159E ILE* 4.7 3.4 - - + -
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Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PRO* 4.5 11.4 - - + -
7E LEU* 4.2 12.8 - - + -
19E VAL* 2.8 32.5 + - + +
22E VAL* 1.3 75.7 - - - +
24E ALA* 1.3 59.1 + - - +
26E ALA* 3.0 11.6 + - - +
28E VAL* 2.8 55.1 + - + +
30E PHE* 3.4 43.7 - - + -
58E VAL* 5.5 2.0 - - + -
60E ILE* 5.9 2.2 - - + -
75E ILE* 3.8 31.4 - - + -
79E HIS* 5.6 1.3 - - + -
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Residues in contact with ALA 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ARG 2.8 17.8 + - - +
21E TRP 3.7 3.1 - - - +
23E LEU* 1.3 74.8 - - - +
25E ALA* 1.3 61.7 + - - +
27E GLY* 2.7 20.7 + - - +
28E VAL 4.4 6.5 - - - +
30E PHE* 4.5 4.2 - - + -
193E THR* 3.3 14.1 - - - +
196E ARG* 5.3 0.3 + - - -
197E PHE* 3.3 40.6 - - + -
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Residues in contact with ALA 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E TRP* 3.0 18.1 + - + +
22E VAL 3.7 4.0 - - - +
24E ALA* 1.3 73.4 - - - +
26E ALA* 1.3 57.1 - - - +
27E GLY 2.8 9.1 + - - -
81E LEU* 5.4 3.4 - - + -
153E LEU* 4.6 13.8 - - + +
158E VAL* 4.3 24.0 - - + -
191E ILE* 5.6 0.3 - - - +
193E THR* 3.2 25.8 + - - +
194E ILE* 4.3 20.0 - - + +
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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