Contacts of the helix formed by residues 16 - 25 (chain C) in PDB entry 1GUL
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.7 26.2 - - + -
8C HIS 3.2 33.0 - - - +
9C TYR* 3.5 29.2 - - + -
13C ARG 3.0 2.9 + - - +
15C ARG* 1.3 74.8 - - - +
17C GLU* 1.3 60.0 + - - +
18C SER 3.1 2.7 - - - -
19C VAL* 2.8 41.7 + - - +
20C ARG* 2.9 29.7 + - - +
56C PRO* 3.5 22.6 - - + +
57C MET 3.7 13.5 - - - +
58C VAL* 4.0 6.7 - - + -
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Residues in contact with GLU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 2.9 38.0 + - + +
14C GLY 4.3 4.5 - - - +
15C ARG 3.3 1.2 - - - -
16C MET* 1.3 77.7 - - - +
18C SER* 1.3 56.6 + - - +
20C ARG* 2.5 41.5 + - - +
21C TRP* 2.8 44.6 + - + +
162C GLN* 3.8 15.9 - - - +
197C PHE* 4.1 2.9 - - - -
204C LYS* 3.5 14.0 + - - +
205C LYS* 2.7 42.4 + - - +
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Residues in contact with SER 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ARG* 4.0 10.3 + - - -
16C MET 3.1 1.0 - - - -
17C GLU* 1.3 76.9 - - - +
19C VAL* 1.3 58.5 + - - +
21C TRP* 3.1 3.9 + - - +
22C VAL* 2.9 33.3 + - - +
68C THR* 5.0 3.2 - - - +
72C LEU* 4.0 16.4 - - - -
100C LEU* 4.6 3.7 - - - +
103C LEU* 3.8 12.8 - - - +
159C ILE* 3.8 16.2 - - - -
162C GLN* 2.7 30.3 + - - +
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 4.4 2.0 - - + -
16C MET* 2.8 39.0 + - - +
18C SER* 1.3 75.7 - - - +
20C ARG* 1.3 64.3 + - - +
22C VAL* 3.8 1.4 - - - +
23C LEU* 3.0 41.4 + - + +
56C PRO* 5.3 0.9 - - + -
58C VAL* 4.4 12.3 - - + -
68C THR* 4.6 13.9 - - + -
71C ILE* 4.4 15.7 - - + -
72C LEU* 3.9 18.6 - - + -
75C ILE* 4.1 15.5 - - + -
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Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 4.0 9.0 - - + -
9C TYR* 3.9 3.6 - - - +
10C PRO 3.7 14.3 + - - -
12C GLY 2.8 29.0 + - - -
13C ARG 3.3 12.9 + - - -
16C MET* 2.9 27.3 + - - +
17C GLU* 2.5 45.3 + - - +
19C VAL* 1.3 76.7 - - - +
21C TRP* 1.3 64.5 + - - +
23C LEU* 3.7 0.7 - - - +
24C ALA* 2.9 25.5 + - - +
30C PHE* 3.9 25.9 - - + -
32C GLU* 2.9 28.0 + - - -
34C PHE* 4.4 0.4 - - - -
197C PHE* 4.0 15.0 - - + -
203C LYS 3.7 16.8 - - - -
205C LYS* 3.6 9.9 - - - +
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Residues in contact with TRP 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 2.8 38.7 + - + +
18C SER* 3.1 10.1 + - - +
20C ARG* 1.3 73.2 - - - +
22C VAL* 1.3 57.2 + - - +
24C ALA* 3.7 1.3 - - - +
25C ALA* 2.8 30.8 + - - +
158C VAL* 3.5 28.8 - - + +
159C ILE* 5.6 0.2 - - + -
161C LEU* 3.4 27.8 - - + -
162C GLN* 3.7 43.8 + - + +
165C LEU* 3.8 26.7 - - + -
194C ILE* 4.1 17.3 - - + -
197C PHE* 3.4 28.5 - + - -
198C LEU* 3.9 13.0 - - + -
204C LYS* 3.9 22.3 - - - +
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER 2.9 21.4 + - - +
19C VAL 3.9 2.5 - - - +
20C ARG 3.2 0.2 - - - -
21C TRP* 1.3 73.2 - - - +
23C LEU* 1.3 68.6 + - - +
25C ALA* 3.3 3.4 + - - +
26C ALA* 2.9 21.8 + - - +
72C LEU* 3.8 14.8 - - + +
75C ILE* 3.8 27.4 - - + -
76C ALA 5.0 2.0 - - - +
81C LEU* 3.8 20.4 - - + +
155C LEU* 3.6 30.3 - - + -
158C VAL* 4.2 16.6 - - + -
159C ILE* 4.4 2.9 - - + -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PRO* 4.5 12.6 - - + -
7C LEU* 4.1 14.4 - - + -
19C VAL* 3.0 34.5 + - + +
20C ARG 3.7 2.7 - - - +
22C VAL* 1.3 77.4 - - - +
24C ALA* 1.3 62.7 + - - +
26C ALA* 3.0 11.5 + - - +
28C VAL* 2.9 50.9 + - + +
30C PHE* 3.7 35.2 - - + -
58C VAL* 5.4 1.6 - - + -
60C ILE* 5.1 3.1 - - + -
75C ILE* 4.0 29.8 - - + -
79C HIS* 5.5 1.6 - - + -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ARG 2.9 13.8 + - - +
21C TRP 3.7 1.6 - - - +
23C LEU* 1.3 75.8 - - - +
25C ALA* 1.3 64.9 + - - +
27C GLY* 2.9 13.0 + - - -
28C VAL 4.1 7.4 + - - +
30C PHE* 4.4 5.3 - - + -
193C THR* 3.2 16.0 - - - +
197C PHE* 3.2 45.5 - - + -
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TRP* 2.8 18.4 + - + +
22C VAL 3.7 4.0 - - - +
24C ALA* 1.3 77.4 - - - +
26C ALA* 1.3 59.0 + - - +
27C GLY 3.0 3.8 + - - -
81C LEU* 5.7 1.6 - - + -
153C LEU* 4.7 13.3 - - + +
158C VAL* 4.0 24.7 - - + -
191C ILE* 5.5 0.5 - - - +
193C THR* 3.0 25.4 + - - +
194C ILE* 4.1 22.0 - - + +
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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