Contacts of the helix formed by residues 21 - 31 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17G GLU* 3.7 15.0 - - - -
18G PRO 4.5 1.0 + - - -
20G ILE* 1.3 78.6 - - - +
22G GLY* 1.3 65.0 + - - +
23G GLN* 3.2 10.5 + - - +
24G ILE* 3.1 33.5 + - - +
25G ASN* 3.3 10.2 + - - -
168G LEU* 5.7 1.0 - - - +
169G GLN* 2.8 28.9 + - - +
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Residues in contact with GLY 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLY* 3.6 13.0 - - - -
13G TYR* 3.5 27.2 - - - +
14G GLY* 4.1 0.2 - - - -
17G GLU* 3.3 23.2 + - - -
21G SER* 1.3 71.0 - - - +
23G GLN* 1.3 66.0 + - - +
24G ILE 3.1 0.2 + - - -
25G ASN* 3.2 2.4 + - - +
26G GLU* 2.9 25.1 + - - +
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Residues in contact with GLN 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLY* 3.6 8.4 - - - +
94A GLU* 1.9 62.3 + - + +
97A ALA* 3.2 31.4 - - + +
98A ALA 5.3 0.2 - - - +
21G SER* 3.2 8.1 + - - +
22G GLY* 1.3 76.0 - - - +
24G ILE* 1.3 63.8 + - - +
26G GLU* 3.4 1.6 + - - +
27G LEU* 3.1 30.5 + - + +
168G LEU* 3.9 22.9 - - + +
171H LYS* 4.2 17.8 - - - +
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Residues in contact with ILE 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ILE* 4.1 14.4 - - + -
21G SER* 3.1 19.8 + - - +
22G GLY 3.1 0.8 - - - -
23G GLN* 1.3 77.3 - - - +
25G ASN* 1.3 60.0 + - - +
26G GLU 2.9 0.7 + - - -
27G LEU* 3.0 4.3 + - - +
28G HIS* 2.8 44.0 + - + +
164G HIS 4.2 14.8 - - - +
165G ALA* 3.9 17.3 - - - +
166G PHE* 4.0 23.6 - - - -
168G LEU* 4.2 22.9 - - + +
169G GLN* 3.8 34.5 - - + +
170G TYR* 5.5 1.1 - - + -
177G PHE* 6.2 0.2 - - + -
167H TYR* 6.1 0.9 - - + -
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Residues in contact with ASN 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G TRP* 4.0 8.0 - - + -
13G TYR* 3.0 40.6 + - + +
16G LEU* 3.4 29.5 - - - +
20G ILE* 3.5 28.0 + - - +
21G SER 3.3 4.8 + - - +
22G GLY 3.2 4.2 + - - +
24G ILE* 1.3 80.5 - - - +
26G GLU* 1.3 58.4 + - - +
28G HIS* 3.8 6.7 + - - +
29G HIS* 3.0 32.4 + - - +
79G TRP* 5.3 1.6 + - - -
80G TRP* 3.9 17.3 - - + -
83G LEU* 5.2 1.4 - - - +
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Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A THR 4.4 1.4 - - - +
93A GLY* 3.3 2.1 - - - -
94A GLU* 2.2 55.7 + - + +
95A LEU 4.8 1.6 + - - -
191A GLN* 5.7 2.8 - - - +
194A TYR* 5.8 2.3 - - - -
195A ALA* 5.2 9.4 - - - +
13G TYR* 3.6 34.5 - - + -
22G GLY 2.9 15.9 + - - +
23G GLN 3.7 2.7 - - - +
24G ILE 2.9 1.0 + - - -
25G ASN* 1.3 76.2 - - - +
27G LEU* 1.3 63.7 + - + +
30G SER* 2.7 38.6 + - - +
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Residues in contact with LEU 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU* 3.7 33.7 - - + +
23G GLN 3.1 19.4 + - - +
24G ILE* 3.0 5.1 + - - +
26G GLU* 1.3 76.9 - - - +
28G HIS* 1.3 60.0 + - - +
30G SER* 4.1 0.4 - - - -
31G LYS* 2.8 47.6 + - + +
32G HIS* 3.1 6.5 + - - -
168G LEU* 3.7 22.7 - - + -
167H TYR* 3.9 17.5 - - + +
171H LYS* 3.8 19.3 - - + -
172H ASN* 3.3 23.3 - - - +
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Residues in contact with HIS 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ILE* 2.8 30.6 + - + +
25G ASN* 3.8 1.7 + - - +
27G LEU* 1.3 79.2 - - - +
29G HIS* 1.3 56.7 + - - +
32G HIS* 3.3 15.1 - - + +
33G HIS* 2.9 28.8 + - - +
76G HIS* 3.0 15.0 + + - -
79G TRP* 3.5 23.7 + + - -
80G TRP* 3.6 19.5 - + + -
160G ASP* 2.9 19.7 + - - -
164G HIS* 3.0 23.3 + + - +
165G ALA* 4.3 6.5 - - + +
999G FE 2.4 26.2 - - - -
167H TYR* 5.1 0.4 + - - -
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Residues in contact with HIS 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LEU* 3.8 29.7 - - + +
7G PRO* 2.9 28.2 + - + -
8G ASP* 5.0 4.3 - - - -
9G LEU* 3.4 34.3 - - + +
13G TYR* 2.9 28.3 + + + -
25G ASN 3.0 19.2 + - - +
28G HIS* 1.3 76.3 - - - +
30G SER* 1.3 63.2 + - - +
33G HIS* 3.3 20.4 - - - +
34G ALA 3.3 6.8 + - - -
80G TRP* 3.6 26.2 - + + -
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Residues in contact with SER 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LEU* 4.9 4.0 - - - -
13G TYR* 4.1 13.0 - - - -
26G GLU* 2.7 28.7 + - - +
27G LEU* 4.1 0.3 - - - +
29G HIS* 1.3 81.5 - - - +
31G LYS* 1.3 79.6 + - - +
34G ALA* 3.5 16.2 - - - +
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Residues in contact with LYS 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ALA 5.6 2.4 + - - -
198A THR 5.7 1.8 + - - -
199A SER* 4.3 16.8 + - - +
27G LEU* 2.8 33.3 + - + +
29G HIS 3.3 0.4 - - - -
30G SER* 1.3 92.3 + - - +
32G HIS* 1.3 64.0 + - - +
33G HIS 3.6 0.4 - - - -
34G ALA* 3.6 2.0 + - - +
35G THR* 2.8 30.4 + - - -
172H ASN* 3.6 44.2 - - + +
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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