Contacts of the helix formed by residues 189 - 200 (chain A) in PDB entry 4GWF
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 SER 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG* 2.8 32.2 + - - -
105A ALA* 3.8 24.0 - - - -
179A TYR* 3.7 14.8 - - - -
187A PHE* 3.2 9.8 - - - +
188A ASP* 1.3 77.6 - - - +
190A LEU* 1.3 62.5 + - - +
191A THR* 3.6 4.5 + - - -
192A ASP* 2.9 21.0 + - - -
193A LEU* 3.2 17.5 + - - +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ALA 4.7 2.8 + - - +
107A PRO* 3.8 25.6 - - + -
112A TRP* 3.9 13.7 - - + -
113A PHE* 4.0 5.8 - - + -
137A VAL* 4.1 9.4 - - + -
147A PHE* 3.6 41.5 - - + -
172A ILE* 3.9 42.2 - - + -
179A TYR* 3.9 20.3 - - + -
189A SER* 1.3 71.0 - - - +
191A THR* 1.4 54.2 + - - +
193A LEU* 3.5 6.8 + - + +
194A VAL* 2.9 38.7 + - + +
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 3.8 33.1 + - - +
104A CYS 5.5 0.7 + - - -
105A ALA 5.3 2.4 + - - -
106A ASP 5.3 1.4 + - - -
107A PRO* 4.8 6.6 - - - +
110A GLU* 3.3 30.4 + - - +
112A TRP* 3.7 14.9 - - + -
189A SER* 3.2 9.9 + - - -
190A LEU* 1.4 74.9 - - - +
192A ASP* 1.3 58.1 + - - +
194A VAL* 4.0 0.2 - - - +
195A GLU* 2.9 48.9 + - + +
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Residues in contact with ASP 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 2.9 25.2 + - - -
103A ASN* 5.7 0.9 + - - -
187A PHE* 3.8 20.9 - - + -
188A ASP* 3.9 12.9 - - - +
189A SER* 2.9 29.5 + - - +
191A THR* 1.3 75.3 - - - +
193A LEU* 1.4 60.7 + - - +
195A GLU* 4.1 3.6 - - - +
196A HIS* 3.2 25.1 + - - +
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 5.8 5.2 - - + -
172A ILE* 3.9 32.3 - - + -
179A TYR* 3.7 38.4 - - + +
180A ASP* 3.7 13.0 - - - +
181A VAL* 4.3 8.3 - - + -
187A PHE* 3.7 22.4 - - + -
189A SER 3.2 11.6 + - - +
190A LEU* 3.6 11.7 - - + +
191A THR 3.3 0.2 - - - -
192A ASP* 1.4 73.8 - - - +
194A VAL* 1.4 71.2 + - + +
196A HIS* 3.4 2.6 + - - +
197A TYR* 3.1 44.8 + - + -
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TRP* 3.9 27.8 - - + +
135A PHE* 3.7 30.5 - - + -
137A VAL* 3.9 28.5 - - + -
149A LEU* 4.9 5.4 - - + -
190A LEU* 2.9 26.1 + - + +
191A THR 4.0 2.7 - - - +
193A LEU* 1.4 80.3 - - + +
195A GLU* 1.3 59.2 + - - +
197A TYR* 3.3 2.8 + - - -
198A LYS* 2.9 37.3 + - + +
212A LEU* 3.7 7.7 - - + +
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Residues in contact with GLU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 4.8 4.9 - - - +
112A TRP* 4.4 9.7 + - - -
191A THR* 2.9 34.4 + - + +
192A ASP* 4.2 4.3 - - - +
194A VAL* 1.3 76.6 - - - +
196A HIS* 1.3 61.5 + - - +
198A LYS* 3.4 34.7 + - - +
199A LYS* 3.2 23.9 + - - +
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Residues in contact with HIS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLU* 3.8 21.7 + - - +
187A PHE* 3.5 27.4 - + + -
192A ASP 3.2 20.6 + - - +
193A LEU 3.6 4.3 - - - +
195A GLU* 1.3 76.4 - - - +
197A TYR* 1.3 74.3 + + - +
199A LYS* 3.3 3.4 + - - -
200A ASN* 2.7 65.4 + - + +
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Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 5.9 0.4 - - + -
181A VAL* 3.4 37.9 + - + +
183A GLY 4.2 8.0 + - - -
184A GLY* 5.4 0.9 - - - -
185A GLU* 4.8 5.7 + - - +
187A PHE* 3.7 26.6 - + - -
193A LEU* 3.1 37.0 + - + +
194A VAL* 3.6 1.1 - - - -
196A HIS* 1.3 89.9 + + - +
198A LYS* 1.4 61.8 + - - +
199A LYS 3.5 0.2 - - - -
200A ASN* 3.3 17.5 - - + -
201A PRO* 3.3 22.7 - - - +
202A MET* 3.6 35.7 - - + +
210A LEU 4.6 0.7 - - - +
212A LEU* 3.7 24.9 + - + +
602A EDO 6.1 4.3 - - - -
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Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TRP* 5.7 1.1 - - + +
135A PHE* 4.3 11.1 - - + -
194A VAL* 2.9 23.7 + - + +
195A GLU* 3.4 46.0 - - - +
196A HIS 3.2 0.2 - - - -
197A TYR* 1.4 76.8 - - - +
199A LYS* 1.3 61.2 + - - +
201A PRO* 4.2 9.2 - - - +
211A GLN* 4.9 4.0 - - - +
212A LEU* 3.5 44.3 + - + +
213A LYS 3.7 14.3 + - - -
214A GLN* 5.3 1.0 - - - +
215A PRO* 5.6 3.0 - - - +
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Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLU 3.2 13.2 + - - +
196A HIS* 3.9 3.4 - - - +
198A LYS* 1.3 79.6 - - - +
200A ASN* 1.4 72.7 + - - +
201A PRO* 3.4 8.6 - - - +
199B LYS* 3.9 30.3 - - - +
200B ASN* 6.2 0.4 - - - +
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Residues in contact with ASN 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A HIS* 2.7 55.5 + - + +
197A TYR* 3.3 25.5 - - + -
199A LYS* 1.4 90.3 - - - +
201A PRO* 1.4 67.7 - - - +
199B LYS* 5.8 4.3 + - - +
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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