Contacts of the helix formed by residues 16 - 25 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D LEU* 3.8 24.7 - - + -
8D HIS 3.1 35.2 - - - +
9D TYR* 3.5 26.7 - - + -
13D ARG 3.2 0.8 + - - -
15D ARG* 1.3 76.9 - - - +
17D GLU* 1.3 58.6 + - - +
18D SER 3.2 1.1 - - - -
19D VAL* 2.7 41.4 + - - +
20D ARG* 3.1 30.2 + - - +
56D PRO* 3.6 21.9 - - + +
57D MET 3.6 17.5 - - - +
58D VAL* 3.8 8.5 - - + -
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 2.9 38.8 + - + +
14D GLY 4.2 5.6 - - - +
15D ARG 3.1 1.2 - - - -
16D MET* 1.3 77.6 - - - +
18D SER* 1.3 58.6 + - - +
19D VAL 2.9 0.6 + - - -
20D ARG* 2.5 45.5 + - - +
21D TRP* 2.8 45.7 + - + +
162D GLN* 3.6 12.1 - - - +
197D PHE* 4.2 2.8 - - - -
204D LYS* 3.5 12.9 + - - +
205D LYS* 2.7 34.6 + - - +
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Residues in contact with SER 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ARG* 3.8 11.0 + - - -
16D MET 3.2 0.8 - - - -
17D GLU* 1.3 78.7 - - - +
19D VAL* 1.3 64.5 + - - +
21D TRP* 3.4 3.8 - - - +
22D VAL* 3.0 27.0 + - - +
68D THR* 5.0 2.9 - - - +
72D LEU* 3.6 12.9 - - - +
100D LEU* 4.6 5.2 - - - +
103D LEU* 3.9 11.8 - - - +
107D ILE* 6.0 0.5 - - - +
159D ILE* 3.7 16.8 - - - +
162D GLN* 2.8 31.1 + - - +
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 4.6 2.7 - - + -
16D MET* 2.7 38.6 + - - +
18D SER* 1.3 78.1 - - - +
20D ARG* 1.3 65.3 + - - +
22D VAL* 3.1 3.1 + - - +
23D LEU* 2.8 35.3 + - + +
56D PRO* 5.5 0.4 - - + -
58D VAL* 4.7 6.1 - - + -
68D THR* 4.3 19.1 - - + -
71D ILE* 4.2 18.6 - - + -
72D LEU* 4.1 15.9 - - + -
75D ILE* 4.1 22.9 - - + -
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Residues in contact with ARG 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D LEU* 4.0 8.7 - - + +
9D TYR* 4.2 3.2 - - - +
10D PRO 3.9 12.1 + - - -
12D GLY 2.7 28.3 + - - -
13D ARG 3.2 10.1 + - - -
16D MET* 3.7 24.4 - - - +
17D GLU* 2.5 45.6 + - - +
19D VAL* 1.3 75.7 - - - +
21D TRP* 1.3 65.7 + - - +
23D LEU* 3.7 0.5 - - - +
24D ALA* 2.8 27.0 + - - +
30D PHE* 3.8 28.0 - - + -
32D GLU* 2.8 27.6 + - - -
34D PHE* 4.1 2.4 - - - -
197D PHE* 4.1 14.6 - - + -
203D LYS 3.5 17.7 - - - -
205D LYS* 3.4 13.9 - - - +
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Residues in contact with TRP 21 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D GLU* 2.8 35.0 + - + +
18D SER* 3.4 12.1 - - - +
20D ARG* 1.3 78.1 - - - +
22D VAL* 1.3 64.0 + - - +
24D ALA* 3.7 2.6 - - - +
25D ALA* 3.0 23.7 + - + +
158D VAL* 3.8 29.8 - - + +
159D ILE* 5.6 0.2 - - + -
161D LEU* 3.5 28.7 - - + -
162D GLN* 3.8 41.6 - - + +
165D LEU* 3.8 25.4 - - + -
194D ILE* 4.4 13.9 - - + -
197D PHE* 3.3 34.9 - + - -
198D LEU* 4.0 12.8 - - + -
204D LYS* 4.1 17.9 - - - +
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Residues in contact with VAL 22 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D SER 3.0 15.8 + - - +
19D VAL* 3.8 2.9 - - - +
21D TRP* 1.3 78.7 - - - +
23D LEU* 1.3 66.6 + - - +
25D ALA* 3.2 3.0 + - - +
26D ALA* 2.9 21.1 + - - +
72D LEU* 3.9 12.3 - - + +
75D ILE* 3.8 23.6 - - + -
76D ALA 5.1 0.9 - - - +
81D LEU* 3.6 27.1 - - + -
155D LEU* 3.5 29.8 - - + -
158D VAL* 4.2 17.3 - - + -
159D ILE* 4.7 3.1 - - + -
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PRO* 4.5 10.8 - - + -
7D LEU* 4.2 12.1 - - + -
19D VAL* 2.8 32.2 + - + +
22D VAL* 1.3 74.7 - - - +
24D ALA* 1.3 57.9 + - - +
26D ALA* 3.0 11.6 + - - +
28D VAL* 2.9 54.2 + - + +
30D PHE* 3.4 44.2 - - + -
58D VAL* 5.5 1.6 - - + -
60D ILE* 5.9 2.7 - - + -
75D ILE* 3.8 32.5 - - + -
79D HIS* 5.6 1.3 - - + -
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ARG 2.8 17.8 + - - +
21D TRP 3.7 2.9 - - - +
23D LEU* 1.3 75.0 - - - +
25D ALA* 1.3 61.5 + - - +
27D GLY* 2.7 21.0 + - - +
28D VAL 4.1 6.3 + - - +
30D PHE* 4.5 4.2 - - + -
193D THR* 3.3 13.6 - - - +
194D ILE* 6.0 0.2 - - - -
196D ARG* 5.3 0.7 + - - -
197D PHE* 3.3 39.9 - - + -
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D TRP* 3.0 18.3 + - + +
22D VAL* 3.2 4.0 + - - +
24D ALA* 1.3 72.5 - - - +
26D ALA* 1.3 56.9 + - - +
27D GLY 2.8 9.2 + - - -
81D LEU* 5.4 3.4 - - + -
153D LEU* 4.6 13.9 - - + +
158D VAL* 4.3 23.6 - - + -
191D ILE* 5.6 0.3 - - - +
193D THR* 3.2 26.7 + - - +
194D 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