Contacts of the helix formed by residues 16 - 25 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B LEU* 3.8 24.5 - - + -
8B HIS 3.1 35.4 - - - +
9B TYR* 3.5 28.2 - - + -
13B ARG 3.2 1.0 + - - -
15B ARG* 1.3 76.5 - - - +
17B GLU* 1.3 59.0 + - - +
18B SER 3.2 1.1 - - - -
19B VAL* 2.7 41.2 + - - +
20B ARG* 3.1 29.4 + - - +
56B PRO* 3.6 20.8 - - + +
57B MET 3.6 17.5 - - - +
58B VAL* 3.8 9.0 - - + -
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 2.9 37.8 + - + +
14B GLY 4.2 5.6 - - - +
15B ARG 3.1 1.2 - - - -
16B MET* 1.3 78.4 - - - +
18B SER* 1.3 58.6 + - - +
19B VAL 3.0 0.2 + - - -
20B ARG* 2.5 45.6 + - - +
21B TRP* 2.8 45.6 + - + +
162B GLN* 3.6 12.8 - - - +
197B PHE* 4.2 2.3 - - - -
204B LYS* 3.5 13.2 + - - +
205B LYS* 2.7 34.8 + - - +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG 3.9 10.3 + - - -
16B MET 3.2 0.8 - - - -
17B GLU* 1.3 78.9 - - - +
19B VAL* 1.3 63.6 + - - +
21B TRP* 3.4 3.8 - - - +
22B VAL* 3.0 27.2 + - - +
68B THR* 5.0 2.9 - - - +
72B LEU* 3.9 12.7 - - - +
100B LEU* 4.6 5.6 - - - +
103B LEU* 3.9 11.6 - - - +
107B ILE* 6.0 0.5 - - - +
159B ILE* 3.7 16.7 - - - +
162B GLN* 2.8 32.5 + - - +
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.6 2.9 - - + -
16B MET* 2.7 39.3 + - - +
18B SER* 1.3 78.0 - - - +
20B ARG* 1.3 64.1 - - - +
22B VAL* 3.1 2.9 + - - +
23B LEU* 2.8 35.4 + - + +
56B PRO* 5.5 0.4 - - + -
58B VAL* 4.7 5.8 - - + -
68B THR* 4.3 18.4 - - + -
71B ILE* 4.2 19.1 - - + -
72B LEU* 4.1 14.8 - - + -
75B ILE* 4.1 22.9 - - + -
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.0 8.7 - - + +
9B TYR* 4.2 3.2 - - - +
10B PRO 3.9 12.5 + - - -
12B GLY 2.7 27.3 + - - -
13B ARG 3.2 10.1 + - - -
16B MET* 3.7 22.7 - - - +
17B GLU* 2.5 46.4 + - - +
19B VAL* 1.3 75.6 - - - +
21B TRP* 1.3 64.7 + - - +
23B LEU* 3.7 0.3 - - - +
24B ALA* 2.8 27.4 + - - +
30B PHE* 3.8 27.7 - - + -
32B GLU* 2.8 27.6 + - - -
34B PHE* 4.1 2.6 - - - -
197B PHE* 4.1 14.8 - - + -
203B LYS 3.5 17.5 - - - -
205B LYS* 3.4 14.1 - - - +
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Residues in contact with TRP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 2.8 35.9 + - + +
18B SER* 3.4 12.3 - - - +
20B ARG* 1.3 77.2 - - - +
22B VAL* 1.3 65.5 + - - +
24B ALA* 3.7 1.6 - - - +
25B ALA* 3.0 24.2 + - + +
158B VAL* 3.8 29.0 - - + +
159B ILE* 5.6 0.2 - - + -
161B LEU* 3.5 27.6 - - + -
162B GLN* 3.8 41.6 + - + +
165B LEU* 3.8 26.7 - - + -
194B ILE* 4.4 14.1 - - + -
197B PHE* 3.3 35.1 - + - -
198B LEU* 4.0 12.8 - - + -
204B LYS* 4.1 17.5 - - - +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER 3.0 16.7 + - - +
19B VAL 3.8 2.2 - - - +
21B TRP* 1.3 77.8 - - - +
23B LEU* 1.3 66.1 + - - +
25B ALA* 3.2 2.9 + - - +
26B ALA* 2.9 21.0 + - - +
72B LEU* 3.9 11.4 - - + +
75B ILE* 3.8 23.6 - - + -
76B ALA 5.1 1.1 - - - +
81B LEU* 3.6 27.6 - - + -
155B LEU* 3.5 30.1 - - + -
158B VAL* 4.2 17.3 - - + -
159B ILE* 4.7 3.8 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 4.5 9.9 - - + -
7B LEU* 4.2 13.0 - - + -
19B VAL* 2.8 32.0 + - + +
22B VAL* 1.3 75.5 - - - +
24B ALA* 1.3 59.3 - - - +
26B ALA* 3.0 11.7 + - - +
28B VAL* 2.8 54.5 + - + +
30B PHE* 3.4 44.9 - - + -
58B VAL* 5.5 2.0 - - + -
60B ILE* 5.9 2.7 - - + -
75B ILE* 3.8 33.2 - - + -
79B HIS* 5.6 1.3 - - + -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG 2.8 18.1 + - - +
21B TRP 3.7 3.4 - - - +
23B LEU* 1.3 76.0 - - - +
25B ALA* 1.3 61.0 + - - +
27B GLY* 2.7 20.4 + - - +
28B VAL 4.4 5.4 - - - +
30B PHE* 4.5 5.3 - - + -
193B THR* 3.3 14.1 - - - +
196B ARG* 5.3 0.3 + - - -
197B PHE* 3.3 39.5 - - + -
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TRP* 3.0 17.4 + - + +
22B VAL 3.7 3.6 - - - +
24B ALA* 1.3 73.8 - - - +
26B ALA* 1.3 58.2 + - - +
27B GLY 2.8 8.5 + - - -
81B LEU* 5.4 3.6 - - + -
153B LEU* 4.6 13.8 - - + +
158B VAL* 4.3 24.9 - - + -
191B ILE* 5.6 0.3 - - - +
193B THR* 3.2 26.4 + - - +
194B 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