Contacts of the helix formed by residues 21 - 31 (chain F) in PDB entry 1GN2
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 SER 21 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F GLU* 3.7 15.3 - - - -
18F PRO 4.5 1.0 + - - -
20F ILE* 1.3 77.4 - - - +
22F GLY* 1.3 65.2 + - - +
23F GLN* 3.2 10.7 + - - +
24F ILE* 3.1 33.9 + - - +
25F ASN* 3.3 10.9 + - - -
168F LEU* 5.7 0.9 - - - +
169F GLN* 2.8 28.6 + - - +
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Residues in contact with GLY 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TYR* 3.5 29.2 - - - +
14F GLY* 4.1 2.0 - - - -
17F GLU* 3.3 22.5 + - - -
20F ILE 3.7 0.2 + - - -
21F SER* 1.3 71.7 - - - +
23F GLN* 1.3 66.0 + - - +
25F ASN* 3.2 2.3 + - - +
26F GLU* 2.9 27.0 + - - +
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Residues in contact with GLN 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E LYS* 4.3 26.1 - - - +
21F SER* 3.2 8.4 + - - +
22F GLY* 1.3 74.9 - - - +
24F ILE* 1.3 63.2 + - - +
26F GLU* 3.4 13.2 + - - +
27F LEU* 3.1 37.7 + - + +
168F LEU* 3.9 25.3 - - + +
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Residues in contact with ILE 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E TYR* 6.3 0.7 - - + -
20F ILE* 4.1 14.1 - - + -
21F SER* 3.1 19.9 + - - +
22F GLY 3.1 0.6 - - - -
23F GLN* 1.3 76.4 - - - +
25F ASN* 1.3 60.6 + - - +
26F GLU 2.9 0.9 + - - -
27F LEU* 3.0 5.0 + - - +
28F HIS* 2.8 42.9 + - + +
164F HIS 4.2 15.7 - - - +
165F ALA* 3.9 16.6 - - - +
166F PHE* 4.0 23.3 - - - -
168F LEU* 4.2 22.7 - - + +
169F GLN* 3.8 36.1 - - + +
170F TYR* 5.5 0.9 - - + -
177F PHE* 6.2 0.4 - - + -
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Residues in contact with ASN 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F TRP* 4.0 8.2 - - + -
13F TYR* 3.0 41.6 + - + +
16F LEU* 3.4 30.0 - - - +
20F ILE* 3.5 27.0 + - - +
21F SER 3.3 3.7 + - - -
22F GLY 3.2 3.8 + - - +
24F ILE* 1.3 79.8 - - - +
26F GLU* 1.3 58.0 + - - +
28F HIS* 3.8 7.2 + - - +
29F HIS* 3.0 31.7 + - - +
79F TRP* 5.3 1.7 + - - -
80F TRP* 3.9 17.0 - - + -
83F LEU* 5.2 1.4 - - - +
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Residues in contact with GLU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TYR* 3.6 36.1 - - + +
22F GLY 2.9 17.7 + - - +
23F GLN* 3.7 13.1 - - - +
24F ILE 2.9 1.2 + - - -
25F ASN* 1.3 75.5 - - - +
27F LEU* 1.3 67.3 + - + +
30F SER* 2.7 38.2 + - - +
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E TYR* 3.7 17.7 - - + +
171E LYS* 3.8 27.4 - - + -
172E ASN* 3.4 24.0 - - - +
23F GLN* 3.1 27.2 + - + +
24F ILE* 3.0 4.6 + - - +
26F GLU* 1.3 80.0 - - + +
28F HIS* 1.3 59.4 - - - +
30F SER* 4.1 0.4 - - - -
31F LYS* 2.8 47.2 + - + +
32F HIS* 3.1 6.1 + - - -
168F LEU* 3.7 27.1 - - + -
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Residues in contact with HIS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ILE* 2.8 30.4 + - + +
25F ASN* 3.8 1.9 + - - +
27F LEU* 1.3 79.6 - - - +
29F HIS* 1.3 56.8 + - - +
32F HIS* 3.3 15.0 - - + +
33F HIS* 2.9 28.8 + - - +
76F HIS* 3.0 15.9 + + - -
79F TRP* 3.5 24.0 + + - -
80F TRP* 3.6 19.4 - + + -
160F ASP* 2.9 19.0 + - - -
164F HIS* 3.0 22.9 + + - +
165F ALA* 4.3 7.1 - - + +
999F FE 2.4 25.1 - - - -
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Residues in contact with HIS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 3.8 29.2 - - + +
7F PRO 2.9 27.8 + - - -
8F ASP* 5.0 4.0 - - - -
9F LEU* 3.4 34.3 - - + +
13F TYR* 2.9 28.1 + + + -
25F ASN 3.0 19.6 + - - +
28F HIS* 1.3 77.4 - - - +
30F SER* 1.3 64.4 + - - +
33F HIS* 3.3 20.2 - - - +
34F ALA 3.3 6.9 + - - -
80F TRP* 3.5 27.8 - + + -
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Residues in contact with SER 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LEU* 4.9 4.5 - - - -
13F TYR* 4.1 12.8 - - - -
26F GLU* 2.7 29.4 + - - +
27F LEU* 4.1 0.3 - - - -
29F HIS* 1.3 79.8 - - - +
31F LYS* 1.3 79.7 + - - +
34F ALA* 3.5 16.1 - - - +
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Residues in contact with LYS 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E ASN* 3.5 46.9 - - + +
27F LEU* 2.8 34.1 + - + +
29F HIS 3.3 0.2 - - - -
30F SER* 1.3 90.6 + - - +
32F HIS* 1.3 64.6 + - - +
34F ALA* 3.6 1.8 + - - +
35F THR* 2.8 31.3 + - - -
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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