Contacts of the helix formed by residues 196 - 206 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85K LYS 3.5 15.4 + - - -
86K ASN* 2.9 31.2 + - - +
87K LEU 3.9 2.2 + - - -
88K ALA* 3.7 27.3 - - + +
92K LYS 5.2 3.4 - - - +
93K GLY 4.9 4.7 - - - +
94K GLY* 4.9 1.6 - - - -
167K ILE* 4.2 1.7 - - - +
194K VAL 3.5 1.2 + - - -
195K ILE* 1.3 73.4 - - - +
197K TRP* 1.3 59.8 + - - +
198K ALA* 3.2 23.0 + - - +
199K GLU* 3.4 20.8 + - - +
200K ALA 3.5 6.8 + - - -
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Residues in contact with TRP 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K GLY 5.2 1.4 + - - -
95K GLY 4.5 3.0 + - - -
96K LYS 3.2 33.6 + - - +
97K HIS* 4.1 12.8 - - - -
98K PRO* 3.6 32.8 - - + -
104K LEU* 4.3 4.2 - - + +
108K ILE* 4.3 15.0 - - + -
115K VAL* 4.0 19.3 - - + -
118K LEU* 4.5 7.9 - - + -
119K ILE* 4.3 5.2 - - + +
137K ILE* 3.9 24.9 - - + -
166K ILE* 5.6 1.6 - - + -
167K ILE* 3.9 14.4 - - + -
192K TRP* 3.5 29.5 + + - -
195K ILE* 3.4 28.1 + - + +
196K ASN* 1.3 70.3 + - - +
198K ALA* 1.4 58.6 + - - +
199K GLU 3.3 0.4 - - - -
200K ALA* 3.2 23.6 + - + +
201K GLU* 3.0 32.9 + - - +
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Residues in contact with ALA 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K LYS 5.4 0.2 + - - -
196K ASN* 3.2 13.4 + - - +
197K TRP* 1.4 75.5 - - - +
199K GLU* 1.3 61.7 + - - +
201K GLU* 3.5 14.4 - - - +
202K SER* 3.1 21.9 + - - -
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Residues in contact with GLU 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K LYS* 3.3 42.0 - - - +
86K ASN* 4.5 0.9 - - - -
196K ASN* 3.4 19.8 + - - +
197K TRP 3.3 0.2 - - - -
198K ALA* 1.3 75.7 - - - +
200K ALA* 1.3 58.4 + - - +
202K SER* 3.3 12.8 + - - -
203K ARG* 2.9 78.6 + - - +
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Residues in contact with ALA 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K LEU* 3.6 17.5 - - + -
166K ILE* 3.5 30.4 + - + +
167K ILE* 3.7 26.2 - - + +
196K ASN 3.5 2.4 + - - -
197K TRP* 3.2 20.1 + - + +
199K GLU* 1.3 77.6 - - - +
201K GLU* 1.3 56.6 + - - +
203K ARG* 3.4 1.7 + - - +
204K TYR* 3.0 25.3 + - - +
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Residues in contact with GLU 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K PRO* 3.3 8.3 - - + +
99K ASP* 2.7 37.0 + - - +
102K SER* 3.5 26.4 + - - +
104K LEU* 3.6 19.2 - - + +
197K TRP 3.0 17.7 + - - +
198K ALA* 3.5 15.0 - - - +
200K ALA* 1.3 73.0 - - - +
202K SER* 1.3 64.7 + - - +
204K TYR* 3.2 3.8 + - - +
205K SER* 3.1 28.3 + - - -
302K SO4 4.8 9.5 + - - +
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Residues in contact with SER 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198K ALA 3.1 10.9 + - - -
199K GLU* 3.4 20.2 + - - -
201K GLU* 1.3 78.8 - - - +
203K ARG* 1.4 56.6 + - - +
205K SER* 3.3 4.7 + - - -
206K ALA* 3.0 30.8 + - - +
302K SO4 5.6 0.9 - - - -
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Residues in contact with ARG 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K LEU* 3.0 49.0 + - - +
85K LYS* 3.4 22.2 - - - +
86K ASN* 2.9 29.1 + - - +
139K LYS* 5.3 0.2 - - - +
164K VAL* 3.8 18.6 - - + +
165K PRO 3.7 20.2 - - - +
166K ILE* 3.1 30.9 + - + -
167K ILE* 4.3 0.8 - - - +
168K ALA 4.6 0.4 - - - +
199K GLU* 2.9 43.1 + - - +
200K ALA 3.6 4.5 - - - +
201K GLU 3.3 0.2 - - - -
202K SER* 1.4 74.2 - - - +
204K TYR* 1.3 60.7 + - - +
206K ALA* 3.7 16.2 + - - +
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Residues in contact with TYR 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ALA* 3.8 26.0 - - + -
104K LEU* 3.6 39.7 - - + +
107K GLN* 3.3 25.4 + - + +
139K LYS* 2.7 74.8 + - + +
144K GLY 4.7 0.2 + - - -
145K GLY* 2.6 28.5 + - - -
147K LEU* 3.9 13.2 - - + -
166K ILE* 3.7 8.5 - - + +
200K ALA 3.0 14.2 + - - +
201K GLU 3.2 8.0 + - - +
203K ARG* 1.3 78.1 - - - +
205K SER* 1.3 57.5 + - - +
206K ALA 3.7 1.2 + - - +
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Residues in contact with SER 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ALA* 4.1 9.3 - - - +
104K LEU 5.2 0.5 + - - -
139K LYS* 5.1 0.4 - - - +
201K GLU 3.1 13.9 + - - -
202K SER* 3.9 4.0 - - - -
204K TYR* 1.3 74.7 - - - +
206K ALA* 1.4 67.3 + - - +
302K SO4 3.0 41.5 + - - -
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Residues in contact with ALA 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K LYS* 5.0 3.8 + - - -
164K VAL* 6.3 0.2 - - + -
202K SER* 3.0 16.6 + - - +
203K ARG* 3.7 14.8 - - - +
204K TYR 3.4 5.0 - - - +
205K SER* 1.4 81.9 - - - +
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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