Contacts of the helix formed by residues 196 - 206 (chain H) in PDB entry 4GUN
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 ASN 196 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85H LYS 3.5 15.0 + - - +
86H ASN* 2.9 26.6 + - - +
87H LEU 3.9 1.8 + - - +
88H ALA* 3.8 28.7 - - + +
92H LYS 5.1 4.9 + - - +
93H GLY* 5.1 4.5 - - - +
94H GLY* 4.9 1.8 - - - -
167H ILE* 4.2 5.0 - - - +
194H VAL 3.6 1.0 + - - -
195H ILE* 1.3 70.3 - - - +
197H TRP* 1.3 60.7 + - - +
198H ALA* 3.3 24.8 + - - +
199H GLU* 3.3 18.8 + - - +
200H ALA* 3.5 9.4 + - - +
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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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93H GLY 5.2 1.8 + - - -
95H GLY 4.7 3.1 + - - -
96H LYS 3.2 31.2 + - - +
97H HIS* 4.2 10.8 - + - -
98H PRO* 3.5 36.1 - - + +
104H LEU* 4.2 6.1 - - + -
108H ILE* 4.2 15.0 - - + -
115H VAL* 3.8 20.6 - - + +
118H LEU* 4.5 8.1 - - + -
119H ILE* 4.1 5.4 - - + +
137H ILE* 4.0 16.2 - - + -
166H ILE* 5.3 1.6 - - + -
167H ILE* 3.9 15.7 - - + -
192H TRP* 3.6 36.4 + + - -
195H ILE* 3.4 28.9 + - + +
196H ASN* 1.3 70.6 + - - +
198H ALA* 1.4 58.8 + - - +
200H ALA* 3.3 17.6 + - + +
201H GLU* 3.0 33.6 + - - +
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Residues in contact with ALA 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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96H LYS 5.4 0.2 + - - -
196H ASN* 3.2 12.5 + - - +
197H TRP* 1.4 75.5 - - - +
199H GLU* 1.4 62.1 + - - +
201H GLU* 3.4 15.3 + - - +
202H SER* 3.2 21.5 + - - -
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Residues in contact with GLU 199 (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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85H LYS* 3.3 41.5 - - - +
86H ASN* 4.4 0.7 - - - +
196H ASN* 3.3 19.2 + - - +
197H TRP 3.3 0.4 - - - -
198H ALA* 1.4 79.4 - - - +
200H ALA* 1.3 55.2 + - - +
202H SER* 3.3 11.5 + - - -
203H ARG* 3.0 75.2 + - - +
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Residues in contact with ALA 200 (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 LEU* 3.6 16.8 - - + -
166H ILE* 3.7 24.6 + - + +
167H ILE* 3.6 28.9 - - + +
196H ASN 3.5 2.2 + - - -
197H TRP* 3.3 16.6 + - + +
199H GLU* 1.3 75.1 - - - +
201H GLU* 1.3 57.9 + - - +
203H ARG* 3.3 4.2 + - - +
204H TYR* 3.0 28.6 + - - +
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Residues in contact with GLU 201 (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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98H PRO* 3.3 16.1 - - + +
99H ASP* 2.8 34.0 + - - +
102H SER* 3.5 31.9 - - - +
104H LEU* 3.6 14.0 + - + +
197H TRP 3.0 17.4 + - - +
198H ALA* 3.5 15.6 - - - +
200H ALA* 1.3 74.4 - - - +
202H SER* 1.3 62.1 + - - +
204H TYR* 3.3 4.0 + - - +
205H SER* 3.2 25.6 + - - -
303H SO4 4.2 12.2 + - - +
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Residues in contact with SER 202 (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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198H ALA 3.2 10.8 + - - -
199H GLU* 3.3 19.0 + - - -
201H GLU* 1.3 78.3 - - - +
203H ARG* 1.4 56.6 + - - +
205H SER* 3.3 6.0 + - - -
206H ALA* 2.9 32.3 + - - +
303H SO4 5.6 0.7 - - - -
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Residues in contact with ARG 203 (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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82H LEU* 2.7 51.6 + - - +
85H LYS* 3.3 21.8 - - - +
86H ASN* 2.8 28.1 + - - +
139H LYS* 5.5 0.3 - - - +
164H VAL* 3.7 18.6 - - + +
165H PRO* 3.6 20.5 + - - +
166H ILE* 3.0 31.1 + - + -
167H ILE* 4.2 0.2 - - - +
168H ALA 4.5 0.6 - - - +
199H GLU* 3.0 41.3 + - - +
200H ALA* 3.3 9.2 + - - +
202H SER* 1.4 76.4 - - - +
204H TYR* 1.3 61.3 + - - +
206H ALA* 3.7 15.2 + - - +
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Residues in contact with TYR 204 (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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103H ALA* 3.8 23.6 - - + -
104H LEU* 3.7 37.2 - - + -
107H GLN* 3.2 25.8 + - + +
139H LYS* 2.8 72.2 + - + +
144H GLY 4.6 0.7 + - - -
145H GLY* 2.6 28.5 + - - -
147H LEU* 3.7 17.9 - - + -
166H ILE* 3.7 9.8 - - + +
200H ALA 3.0 13.6 + - - +
201H GLU 3.6 8.5 - - - +
202H SER 3.3 0.2 - - - -
203H ARG* 1.3 77.3 - - - +
205H SER* 1.3 56.8 + - - +
206H ALA 3.5 1.4 + - - +
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Residues in contact with SER 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H ALA* 3.5 21.5 - - - +
139H LYS* 5.2 0.2 - - - +
201H GLU 3.2 13.6 + - - -
202H SER* 3.7 5.4 - - - -
204H TYR* 1.3 73.3 - - - +
206H ALA* 1.4 66.1 + - - +
303H SO4 2.9 29.3 + - - -
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Residues in contact with ALA 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H LYS* 5.4 2.3 + - - -
202H SER* 2.9 19.6 + - - +
203H ARG* 3.9 13.2 - - - +
204H TYR 3.5 4.3 - - - +
205H SER* 1.4 81.1 - - - +
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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