Contacts of the helix formed by residues 119 - 125 (chain H) in PDB entry 3G3B
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 ASP 119 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128E SER* 3.8 36.2 - - - +
129E GLN* 4.7 3.3 + - - +
131E PRO* 5.5 0.9 - - - +
155E ARG* 5.7 0.6 - - - +
118H THR* 1.3 72.7 - - - +
120H VAL* 1.3 52.6 + - - +
121H GLN* 3.1 8.2 + - - +
122H ALA* 2.8 43.9 + - - +
123H TRP* 4.7 1.3 - - - -
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Residues in contact with VAL 120 (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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24H SER* 3.7 11.2 - - - +
26H GLY* 3.3 20.4 - - - +
27H ASN* 3.6 40.8 - - - +
115H CYS* 2.9 40.2 - - + +
116H LYS* 4.9 1.1 - - - -
117H GLY 5.3 0.7 - - - +
118H THR* 3.0 15.5 + - - +
119H ASP* 1.3 73.6 - - - +
121H GLN* 1.3 64.4 + - + +
122H ALA 3.0 0.7 - - - -
123H TRP* 3.1 27.9 + - + -
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Residues in contact with GLN 121 (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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18H ASP* 4.7 6.1 + - - -
24H SER* 3.2 33.6 + - - +
25H LEU* 4.2 5.7 - - - +
26H GLY* 2.9 29.2 + - - +
119H ASP* 3.1 7.9 + - - +
120H VAL* 1.3 77.4 - - + +
122H ALA* 1.3 63.8 + - - +
123H TRP 3.2 0.7 - - - -
124H ILE* 3.2 33.8 + - + +
125H ARG* 3.5 7.4 + - - +
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Residues in contact with ALA 122 (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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128E SER 3.1 24.7 - - - +
129E GLN* 3.9 14.3 - - - +
131E PRO* 4.1 10.1 - - + -
132E TRP* 3.5 15.6 - - - -
119H ASP* 2.8 27.0 + - - +
121H GLN* 1.3 78.6 - - - +
123H TRP* 1.3 56.7 + - - +
124H ILE 3.1 4.5 + - - -
125H ARG* 3.1 25.6 + - - +
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Residues in contact with TRP 123 (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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131E PRO* 3.6 33.4 - - + +
132E TRP* 3.7 47.8 - + + -
140E LEU* 5.0 0.4 - - + -
5H ARG* 3.0 37.9 + - + +
9H ALA* 4.7 0.9 - - - +
26H GLY* 3.9 10.8 - - - +
29H VAL* 3.9 21.4 - - + +
30H CYS* 3.2 39.8 - - + -
33H LYS* 3.6 36.8 - - + -
34H PHE* 4.2 11.2 - + - -
38H PHE* 4.4 3.6 - + - -
118H THR* 5.0 5.1 + - - -
119H ASP 4.7 1.1 + - - -
120H VAL* 3.1 33.3 + - - +
122H ALA* 1.3 73.6 - - - +
124H ILE* 1.3 62.5 + - - +
127H CYS* 4.7 1.6 - - - -
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Residues in contact with ILE 124 (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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9H ALA* 3.2 33.9 - - + -
25H LEU* 3.6 25.1 - - + -
26H GLY* 3.7 22.7 - - - +
29H VAL* 4.1 7.6 - - + -
121H GLN* 3.2 24.6 + - + +
122H ALA 3.1 0.6 - - - -
123H TRP* 1.3 79.6 - - - +
125H ARG* 1.3 64.1 + - - +
127H CYS* 2.9 30.8 + - + +
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Residues in contact with ARG 125 (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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129E GLN* 3.8 49.4 + - - +
130E HIS* 3.9 24.7 + - - -
132E TRP* 4.8 2.3 - - + -
5H ARG* 3.0 27.4 + - - -
121H GLN 3.5 6.5 + - - +
122H ALA* 3.1 19.6 + - - +
124H ILE* 1.3 77.5 - - - +
126H GLY* 1.3 67.9 + - - +
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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