Contacts of the helix formed by residues 189 - 198 (chain H) in PDB entry 1P7G
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 189 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182H TYR* 4.9 0.9 - - - -
186H TYR* 3.0 21.8 + - + +
187H LYS* 5.7 0.5 - - - +
188H ASN* 1.3 80.1 + - - +
190H ARG* 1.3 65.2 + - - +
191H GLY 3.2 2.2 + - - +
192H SER* 4.1 24.2 + - - +
193H TYR* 3.5 19.6 + - - +
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Residues in contact with ARG 190 (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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133H ALA 3.7 9.0 - - - -
134H LYS* 3.5 32.8 + - + -
136H VAL* 2.8 36.4 + - - +
138H GLY 3.6 14.5 + - - -
177H VAL* 2.8 29.6 + - + +
179H GLU* 4.6 9.9 - - - +
182H TYR* 2.7 41.0 + - + +
188H ASN 2.6 12.9 + - - +
189H ASP* 1.3 73.2 - - - +
191H GLY* 1.3 66.4 + - - +
193H TYR* 3.6 3.7 + - + +
194H VAL* 3.0 33.8 + - + +
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Residues in contact with GLY 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H LYS* 3.7 26.6 - - - +
189H ASP* 3.2 1.6 - - - +
190H ARG* 1.3 77.1 - - - +
192H SER* 1.3 54.9 + - - +
194H VAL* 2.7 25.5 + - - +
195H ASP* 2.8 21.0 + - - +
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Residues in contact with SER 192 (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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186H TYR* 4.0 11.0 - - - -
189H ASP* 3.8 24.0 + - - +
190H ARG 3.7 0.4 - - - -
191H GLY* 1.3 70.5 - - - +
193H TYR* 1.3 53.3 + - - +
195H ASP* 3.4 9.7 + - - -
196H ASN* 2.6 49.4 + - - +
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Residues in contact with TYR 193 (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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33H TYR 5.0 1.8 - - - -
34H ILE* 4.8 17.3 - - + -
93H PHE* 4.0 10.0 - - - -
175H LEU* 3.5 25.6 - - + +
176H ASP 2.7 27.0 + - - -
177H VAL* 4.3 5.2 - - + -
181H ALA* 3.6 22.5 - - + +
182H TYR* 3.8 32.1 - + + -
186H TYR* 3.5 37.3 - + + -
189H ASP 3.5 12.9 + - - +
190H ARG* 3.6 11.9 - - - +
191H GLY 3.1 0.4 - - - -
192H SER* 1.3 78.7 - - - +
194H VAL* 1.3 73.6 + - + +
196H ASN* 3.3 1.9 + - - +
197H TRP* 2.8 33.7 + + + +
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Residues in contact with VAL 194 (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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130H SER* 4.1 24.7 - - - +
133H ALA* 4.3 4.9 - - + -
134H LYS* 4.0 22.2 - - + -
175H LEU* 3.8 26.7 - - + -
177H VAL* 4.2 12.6 - - + -
190H ARG* 3.0 20.5 + - + +
191H GLY 2.7 13.6 + - - +
193H TYR* 1.3 85.3 - - + +
195H ASP* 1.3 62.4 + - - +
197H TRP* 3.1 21.2 + - - +
198H TRP* 3.4 12.6 - - + +
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Residues in contact with ASP 195 (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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126H LYS* 5.0 5.6 + - - +
130H SER* 4.9 4.9 + - - -
134H LYS* 3.3 25.1 + - - -
191H GLY* 2.8 32.2 + - - +
192H SER* 3.4 9.3 + - - +
194H VAL* 1.3 70.2 - - - +
196H ASN* 1.3 64.1 + - - +
197H TRP 3.0 5.8 + - - -
198H TRP* 3.4 26.7 + - + +
199H ASN* 3.7 7.3 + - - +
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Residues in contact with ASN 196 (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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32H PRO 4.2 10.1 + - - -
33H TYR* 3.2 34.0 - - + +
186H TYR* 3.5 30.1 + - - +
192H SER* 2.6 37.0 + - - +
193H TYR 3.5 2.5 - - - +
195H ASP* 1.3 73.7 - - - +
197H TRP* 1.3 61.8 + - - +
199H ASN* 3.4 17.9 + - - +
200H VAL* 4.3 0.2 - - - +
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Residues in contact with TRP 197 (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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33H TYR* 5.5 1.6 - - - -
34H ILE* 4.9 9.6 - - + -
93H PHE* 4.0 6.7 - + - -
96H ASN* 5.2 3.4 - - + -
97H MSE 3.6 33.0 - - + +
129H PHE* 3.6 27.6 - + - -
173H LEU* 3.6 33.2 - - + -
174H ALA 3.8 13.7 - - - -
175H LEU* 3.5 33.6 - - + +
193H TYR* 2.8 17.6 + + + +
194H VAL* 3.1 16.6 - - - +
196H ASN* 1.3 75.0 - - - +
198H TRP* 1.3 84.3 + + - +
199H ASN 2.9 5.2 - - - -
200H VAL* 2.7 36.2 + - + +
201H VAL* 3.5 28.3 + - + -
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Residues in contact with TRP 198 (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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104H GLY* 3.3 20.0 - - - +
105H GLY 5.7 0.2 - - - -
122H PHE* 4.5 8.1 - + + -
125H PHE* 3.7 26.2 - + - -
126H LYS* 2.9 51.3 - - + +
129H PHE* 3.4 36.6 - + + -
130H SER* 2.9 30.0 + - - -
173H LEU* 4.4 2.2 - - + -
194H VAL* 3.4 22.0 + - + +
195H ASP* 3.4 16.2 + - - +
197H TRP* 1.3 99.5 - + - +
199H ASN* 1.3 60.3 + - - +
200H VAL 3.1 4.5 + - - -
201H VAL* 3.7 16.2 + - + +
203H TRP* 3.9 21.6 + + - -
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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