Contacts of the helix formed by residues 162 - 165 (chain H) 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 TRP 162 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G GLY* 3.1 40.4 - - - -
123G CYS* 4.7 1.8 - - - -
163G GLU* 3.9 15.3 - - - -
36H TYR* 3.8 16.8 - - - -
68H PHE* 4.1 7.6 - + - -
123H CYS* 3.6 18.2 - - + -
124H GLY 3.4 23.9 - - - +
125H TRP* 4.1 5.2 - - - -
144H ASP* 2.9 38.0 + - + -
145H HIS* 3.7 22.3 - + - -
160H ASP* 2.8 16.5 + - - +
161H MET* 1.3 81.6 - - - +
163H GLU* 1.3 66.4 + - - +
164H HIS* 3.5 33.4 - + + +
165H ALA* 2.9 15.1 + - - +
166H PHE* 3.2 7.3 - - - -
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Residues in contact with GLU 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G HIS* 4.3 7.8 - - - -
162G TRP* 3.8 18.9 - - - -
163G GLU* 3.4 23.2 + - + +
164G HIS* 2.7 58.1 + - - +
167G TYR* 5.8 0.2 - - - -
122H GLY 6.1 0.9 - - - +
123H CYS* 5.0 10.4 - - - -
161H MET 3.5 1.5 + - - +
162H TRP* 1.3 73.4 - - - +
164H HIS* 1.3 59.8 + - - +
165H ALA 2.9 0.9 + - - -
166H PHE* 3.1 20.2 + - + -
167H TYR* 2.9 44.6 + - + +
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Residues in contact with HIS 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G GLU* 2.6 39.4 + - - +
167G TYR* 3.8 27.2 + - + -
24H ILE* 4.2 13.2 - - - +
28H HIS* 3.0 22.9 + + - +
32H HIS* 3.7 35.1 + + + +
36H TYR* 4.4 9.9 - - - -
76H HIS* 4.6 1.6 - + - -
160H ASP* 3.4 1.3 + - - -
162H TRP* 3.5 29.0 - + + +
163H GLU* 1.3 72.8 - - - +
165H ALA* 1.3 66.0 + - + +
166H PHE 3.3 0.9 + - - -
167H TYR 4.6 0.6 + - - -
168H LEU 5.8 0.2 + - - -
999H FE 2.1 32.3 - - - -
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Residues in contact with ALA 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ILE* 5.2 1.0 - - - +
24H ILE* 3.9 17.6 - - - +
28H HIS* 4.3 8.7 - - + -
79H TRP* 5.3 2.3 - - + -
160H ASP* 3.5 43.1 - - + +
162H TRP 2.9 15.5 + - - +
164H HIS* 1.3 83.4 - - + +
166H PHE* 1.3 63.2 + - + +
177H PHE* 3.6 17.2 - - + -
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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