Contacts of the helix formed by residues 15 - 23 (chain B) in PDB entry 3GUU
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 ASN 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO* 1.3 73.1 - - - +
16B PRO* 1.4 64.3 - - - +
17B TYR* 3.0 40.5 + - - +
18B ASP* 2.7 34.3 + - - +
19B ASP* 3.5 3.8 + - - +
100B ASP* 2.8 30.5 + - - +
105B TYR* 3.8 18.4 + - - +
114B PRO* 5.2 1.4 - - - +
270B ARG* 3.2 34.3 - - - +
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Residues in contact with PRO 16 (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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14B PRO 3.8 0.9 - - - +
15B ASN* 1.4 90.5 - - - +
17B TYR* 1.3 58.9 + - - +
18B ASP 3.2 0.7 + - - -
19B ASP* 3.3 20.2 + - + +
22B TYR* 3.7 43.4 - - + +
99B LEU* 3.7 26.0 - - + +
100B ASP* 4.0 9.4 - - + -
102B ALA* 5.1 0.4 - - + -
105B TYR* 3.5 47.1 - - + -
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN* 3.0 21.6 + - - +
16B PRO* 1.3 77.3 - - - +
18B ASP* 1.3 62.1 + - - +
19B ASP 3.4 1.4 + - - -
98B ALA* 3.7 10.0 - - - +
99B LEU* 3.0 40.3 + - + +
100B ASP* 3.6 30.1 - - + -
268B ARG 3.9 10.7 + - - -
270B ARG* 3.5 46.9 - - + +
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 4.3 14.8 - - + +
15B ASN* 2.7 21.6 + - - +
17B TYR* 1.3 75.7 - - - +
19B ASP* 1.3 56.5 + - - -
20B PRO* 4.0 6.7 - - - +
270B ARG* 2.9 41.4 + - - -
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Residues in contact with ASP 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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13B LEU* 4.7 1.7 - - - +
14B PRO* 3.7 25.7 - - + +
15B ASN 3.7 12.1 - - - +
16B PRO* 3.3 19.0 + - + +
17B TYR 3.4 1.9 + - - +
18B ASP* 1.3 77.2 - - - +
20B PRO* 1.4 66.6 - - - +
21B PHE* 3.0 24.2 + - - +
22B TYR* 3.1 19.0 + - + +
23B THR* 4.3 3.3 - - - +
40B ARG* 2.9 37.1 + - - -
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Residues in contact with PRO 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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18B ASP 4.0 5.8 - - - +
19B ASP* 1.4 85.0 - - - +
21B PHE* 1.3 63.5 + - - +
22B TYR 3.1 0.9 - - - -
23B THR* 2.7 37.7 + - + +
38B GLN* 5.5 1.1 + - - -
58B GLN* 4.2 2.1 + - - -
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Residues in contact with PHE 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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19B ASP* 3.0 17.1 + - - +
20B PRO* 1.3 78.9 - - - +
22B TYR* 1.3 58.0 + + + +
23B THR 3.3 0.2 + - - -
38B GLN* 3.7 44.4 - - + +
39B SER 4.4 4.5 - - - -
40B ARG* 3.4 48.9 - - + +
56B GLN* 3.6 40.6 - - + -
58B GLN* 2.8 50.3 + - + +
72B VAL* 3.8 21.8 - - + +
145B PHE* 4.0 0.7 - - - -
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Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO 5.8 0.9 - - - -
16B PRO* 3.7 53.1 - - + +
19B ASP* 3.1 13.2 + - + +
21B PHE* 1.3 78.5 - - + +
23B THR* 1.3 66.8 + - - +
40B ARG* 3.8 19.9 + - - -
56B GLN* 3.9 8.3 + - - -
72B VAL* 3.9 13.2 - - + -
99B LEU* 4.2 22.2 - - + +
102B ALA* 4.5 5.8 - - + -
104B SER* 2.7 36.3 + - - -
105B TYR* 3.6 12.5 + + - +
108B LEU* 5.9 0.2 - - - +
141B ASP* 3.5 11.2 - - - -
145B PHE* 3.6 35.8 - + + +
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Residues in contact with THR 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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19B ASP 4.3 3.1 - - - +
20B PRO* 2.7 35.4 + - + +
21B PHE 3.3 1.2 + - - -
22B TYR* 1.3 82.6 - - - +
24B THR* 1.3 64.0 + - - +
25B PRO* 3.6 2.6 - - - +
58B GLN* 3.2 21.0 + - - -
70B ALA* 4.2 0.3 - - - +
145B PHE* 3.5 11.6 - - - -
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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
------------------------------------------------------------
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