Contacts of the helix formed by residues 192 - 198 (chain C) in PDB entry 1GUM
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 PRO 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190C ASN 3.0 9.6 - - - +
191C ILE* 1.3 97.1 - - + -
193C THR* 1.4 52.7 + - + +
195C LYS* 3.0 8.9 + - + +
196C ARG* 2.7 58.6 + - - +
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Residues in contact with THR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ALA* 3.3 23.6 - - - +
25C ALA* 3.2 25.3 + - - +
26C ALA 4.5 0.7 - - - -
27C GLY* 3.7 14.8 - - - -
191C ILE* 3.5 18.0 - - + +
192C PRO* 1.4 73.4 - - + +
194C ILE* 1.3 60.2 + - - +
196C ARG* 3.0 28.6 + - - +
197C PHE* 2.8 31.9 + - - +
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Residues in contact with ILE 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TRP* 4.4 10.1 - - + -
25C ALA* 4.3 21.3 - - + +
153C LEU* 4.9 10.1 - - + -
158C VAL* 5.7 4.3 - - + -
161C LEU* 4.0 20.4 - - + -
188C LEU* 3.4 29.2 - - + +
189C SER* 3.7 5.6 - - - -
191C ILE* 3.0 21.8 - - + +
193C THR* 1.3 85.0 + - - +
195C LYS* 1.3 60.1 - - - +
196C ARG 2.9 1.6 - - - -
197C PHE* 2.9 7.5 + - - +
198C LEU* 2.7 60.7 + - + +
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Residues in contact with LYS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C SER 3.4 18.6 - - - +
190C ASN* 3.7 28.5 - - + +
191C ILE 2.4 21.6 + - - +
192C PRO* 3.3 12.3 - - + +
194C ILE* 1.3 72.6 - - - +
196C ARG* 1.3 64.5 + - + +
198C LEU* 3.1 6.9 + - - +
199C GLU* 2.9 48.7 + - + +
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Residues in contact with ARG 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ALA 5.3 0.8 + - - -
27C GLY* 5.3 3.6 - - - -
192C PRO* 2.7 26.8 + - - +
193C THR* 3.0 53.0 + - - +
194C ILE 2.9 0.2 - - - -
195C LYS* 1.3 75.2 - - + +
197C PHE* 1.3 60.2 - - - +
198C LEU 2.9 2.0 - - - -
199C GLU* 2.8 44.0 + - - +
200C PRO 4.6 1.9 - - - +
202C SER* 3.9 4.9 - - - -
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Residues in contact with PHE 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 4.2 1.8 - - - -
20C ARG* 4.1 23.6 - - + -
21C TRP* 3.3 55.6 - + - -
24C ALA* 3.3 31.2 - - + -
30C PHE* 5.3 1.8 - + - -
193C THR 2.8 12.9 + - - +
194C ILE* 3.3 12.1 - - - +
196C ARG* 1.3 77.2 - - - +
198C LEU* 1.3 60.3 + - + +
199C GLU 3.4 0.2 - - - +
202C SER* 2.5 34.0 + - - -
203C LYS* 4.2 5.2 - - + -
204C LYS* 3.2 56.1 - - + +
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TRP* 4.0 23.6 - - + -
161C LEU* 5.3 0.2 - - + -
165C LEU* 4.3 12.8 - - + -
189C SER* 3.5 28.5 - - - +
194C ILE* 2.7 39.2 + - + +
195C LYS* 3.4 5.2 - - - +
197C PHE* 1.3 78.4 - - + +
199C GLU* 1.3 65.7 + - + +
200C PRO* 4.4 1.4 - - - +
204C LYS* 4.2 21.9 - - + +
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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