Contacts of the helix formed by residues 187 - 199 (chain A) in PDB entry 6HBU
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ARG* 4.9 4.7 - - - +
185A GLY 3.6 3.6 + - - -
186A VAL* 1.3 77.8 - - - +
188A GLY* 1.3 60.4 + - - +
190A GLU* 3.2 33.2 + - - +
191A ARG* 2.8 28.9 + - - +
83B GLY 4.0 0.9 + - - -
1501B ATP 3.3 54.6 + - - -
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Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ASP* 4.2 5.7 - - - +
187A SER* 1.3 76.9 - - - +
189A GLY* 1.3 57.5 + - - +
191A ARG* 3.8 24.7 + - - +
192A LYS* 3.2 22.3 + - - +
215A GLY* 4.9 3.0 - - - -
126B GLN* 4.3 18.6 + - - -
127B ASP* 5.5 0.7 - - - -
1501B ATP 3.8 9.2 + - - -
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Residues in contact with GLY 189 (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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188A GLY* 1.3 75.3 - - - +
190A GLU* 1.3 61.5 + - - +
191A ARG 3.3 0.4 - - - -
192A LYS* 3.4 8.1 + - - +
193A ARG* 3.2 33.4 + - - -
215A GLY 3.5 17.8 + - - -
216A LEU* 3.5 9.3 - - - +
82B THR* 4.5 0.9 - - - -
126B GLN* 5.0 0.2 - - - +
1501B ATP 3.1 22.4 + - - -
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Residues in contact with GLU 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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169A GLY 5.7 0.2 - - - +
170A LEU* 3.6 8.1 - - + +
172A LYS* 5.7 2.1 - - - +
173A VAL* 3.3 30.3 - - + +
186A VAL* 3.6 12.9 - - + +
187A SER* 3.2 20.8 + - - +
189A GLY* 1.3 78.4 - - - +
191A ARG* 1.3 51.2 + - - +
192A LYS 3.4 0.2 - - - -
193A ARG* 3.3 25.3 + - - +
194A THR* 2.8 31.4 + - - -
82B THR 4.1 2.3 - - - +
83B GLY* 3.6 14.1 - - - +
1501B ATP 2.7 41.1 + - - -
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Residues in contact with ARG 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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128A ASP* 3.9 25.0 + - + +
130A VAL* 3.7 28.9 - - + +
178A VAL* 4.0 14.4 - - + -
179A GLY* 5.2 7.3 + - - +
186A VAL* 3.5 19.6 + - + +
187A SER 2.8 19.5 + - - +
188A GLY* 3.8 24.2 + - - +
190A GLU* 1.3 75.1 - - - +
192A LYS* 1.3 63.7 + - - +
194A THR* 3.3 7.2 + - - -
195A SER* 3.2 21.7 + - - -
127B ASP* 3.3 35.6 + - - -
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Residues in contact with LYS 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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124A VAL* 4.9 3.7 - - - +
125A VAL 3.5 10.7 + - - -
126A GLN* 3.3 24.4 + - - +
128A ASP* 3.3 22.1 + - - +
188A GLY 3.2 16.5 + - - +
189A GLY* 3.5 12.8 - - - +
190A GLU 3.4 0.2 - - - -
191A ARG* 1.3 77.4 - - - +
193A ARG* 1.3 58.2 + - - +
195A SER* 3.1 6.3 + - - -
196A ILE* 2.9 32.4 + - + +
210A ASP 3.4 12.5 + - - -
211A GLN 3.2 26.8 + - - -
212A PRO* 3.8 24.9 - - - +
214A THR* 4.0 19.3 + - - +
216A LEU* 4.7 6.3 - - + -
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Residues in contact with ARG 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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168A LEU* 2.7 55.3 + - + +
169A GLY* 3.3 21.0 + - - -
170A LEU* 3.9 17.9 - - + +
189A GLY 3.2 14.5 + - - +
190A GLU* 3.3 29.9 + - - +
192A LYS* 1.3 73.4 - - - +
194A THR* 1.3 60.8 + - - +
196A ILE* 3.7 13.2 - - + +
197A GLY* 3.0 21.0 + - - -
216A LEU* 3.8 19.0 - - + +
220A THR* 3.6 28.6 + - - +
224A VAL* 4.7 3.4 - - + -
82B THR* 3.0 28.2 + - - -
304B ALA* 5.1 1.0 - - - +
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Residues in contact with THR 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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130A VAL* 4.4 21.5 - - + -
136A VAL* 3.6 38.0 - - + +
139A ASN* 4.5 3.1 - - + -
140A LEU* 3.9 20.2 - - + +
170A LEU* 4.2 6.6 - - - +
178A VAL* 4.6 3.3 - - + +
190A GLU 2.8 16.6 + - - -
191A ARG* 3.3 12.5 + - - -
192A LYS 3.2 0.6 - - - -
193A ARG* 1.3 77.6 - - - +
195A SER* 1.3 61.3 + - - +
197A GLY* 3.3 1.6 + - - -
198A MET* 3.1 28.1 + - + +
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Residues in contact with SER 195 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A VAL* 4.0 15.1 - - - +
125A VAL* 5.4 4.3 - - - -
128A ASP* 3.3 36.9 + - - +
129A VAL 4.5 2.1 + - - -
130A VAL* 4.4 5.2 - - - +
191A ARG 3.2 8.8 + - - -
192A LYS 3.1 10.4 + - - -
194A THR* 1.3 75.7 - - - +
196A ILE* 1.3 63.8 + - - +
198A MET* 3.6 17.1 + - - +
199A GLU* 2.8 26.9 - - - +
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A VAL* 4.1 20.4 - - + +
168A LEU* 4.2 12.8 - - + -
192A LYS* 2.9 25.5 + - + +
193A ARG* 3.8 20.0 - - + +
195A SER* 1.3 79.0 - - - +
197A GLY* 1.3 61.3 + - - +
198A MET 3.4 0.5 + - - -
199A GLU* 3.5 5.0 + - - +
200A LEU* 3.2 39.2 + - + +
209A LEU* 4.4 13.7 - - + -
212A PRO* 3.4 38.8 - - + +
216A LEU* 4.8 0.9 - - + -
224A VAL* 4.4 16.6 - - + -
228A LEU* 5.9 0.9 - - + -
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Residues in contact with GLY 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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140A LEU* 3.3 19.4 - - - +
164A VAL* 4.0 5.3 - - - +
168A LEU* 3.6 21.5 - - - -
193A ARG 3.0 12.3 + - - -
194A THR 3.3 2.0 + - - -
195A SER 3.3 0.2 - - - -
196A ILE* 1.3 75.7 - - - +
198A MET* 1.3 62.9 + - - +
200A LEU* 3.7 6.5 - - - +
201A ILE* 3.2 21.1 + - - +
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Residues in contact with MET 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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129A VAL 4.6 7.2 - - - +
130A VAL* 3.7 29.4 - - + -
139A ASN* 3.4 40.2 - - - +
140A LEU* 3.8 12.6 - - + -
143A SER* 2.8 27.1 + - - +
147A ARG* 3.9 1.4 + - - -
194A THR* 3.1 20.7 + - + +
195A SER* 3.8 14.4 - - - +
196A ILE 3.4 0.6 - - - -
197A GLY* 1.3 77.0 - - - +
199A GLU* 1.3 65.8 + - - +
200A LEU 3.2 0.4 - - - -
201A ILE* 3.4 13.8 - - - +
202A THR* 3.4 6.6 - - - +
457A HIS* 6.1 2.9 - - + -
463A TYR* 4.4 15.9 - - - +
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Residues in contact with GLU 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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122A GLY* 4.3 6.2 - - - -
123A TYR 3.6 34.9 - - - +
124A VAL* 3.7 21.2 - - + +
147A ARG* 3.5 29.4 + - - +
195A SER* 2.8 24.1 - - - +
196A ILE 3.5 3.2 + - - -
197A GLY 3.3 0.4 - - - -
198A MET* 1.3 83.4 - - - +
200A LEU* 1.3 57.7 + - - +
202A THR* 4.0 8.3 - - - -
204A PRO* 3.9 7.6 - - - +
207A LEU* 3.8 20.0 - - + +
457A HIS* 3.9 22.6 - - - -
461A SER* 3.9 5.9 + - - -
463A TYR* 4.6 2.9 + - - -
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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