Contacts of the helix formed by residues 208 - 228 (chain A) in PDB entry 1H9T
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 VAL 208 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 3.5 35.2 - - + +
113A ILE* 4.8 12.3 - - + +
114A ARG* 4.3 28.0 - - + +
117A PHE* 5.1 8.3 - - + -
196A LEU* 5.4 6.7 - - + -
199A LEU* 5.1 3.6 - - + -
205A HIS* 3.2 20.6 - - - +
206A ASP 2.6 8.4 + - - +
207A GLN* 1.3 75.4 - - - +
209A TYR* 1.3 67.8 + - + +
210A GLU* 2.5 16.3 + - - +
211A THR* 2.6 25.9 + - - -
212A VAL* 3.3 9.8 + - + -
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Residues in contact with TYR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ASN* 5.4 2.5 - - - -
110A THR* 4.2 25.6 - - + -
206A ASP 3.8 5.1 + - - +
208A VAL* 1.3 84.3 - - + +
210A GLU* 1.3 63.8 + - + +
213A ARG* 3.0 80.7 + - + +
111B ILE* 6.3 3.6 - - + -
114B ARG* 5.3 9.9 + - - -
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Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 3.3 23.6 - - - +
207A GLN* 3.1 39.7 - - - +
208A VAL 2.5 4.2 + - - -
209A TYR* 1.3 81.3 - - + +
211A THR* 1.3 68.2 + - - +
213A ARG* 4.0 2.1 - - - +
214A ARG* 3.6 23.7 + - - +
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Residues in contact with THR 211 (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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192A PHE* 3.7 26.5 - - + -
195A LYS* 4.7 19.0 - - + -
196A LEU* 4.3 15.5 - - + +
207A GLN* 3.4 19.6 + - - +
208A VAL* 2.6 13.6 + - - -
210A GLU* 1.3 73.0 + - - +
212A VAL* 1.3 57.0 + - - +
214A ARG* 2.6 47.2 + - - +
215A TYR* 2.9 10.7 + - + -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 6.4 0.2 - - - +
106A THR* 3.6 16.5 - - + +
109A SER* 3.3 22.9 - - - +
110A THR* 3.3 23.8 - - + -
113A ILE* 4.0 21.5 - - + -
149A PHE* 5.9 1.3 - - + -
192A PHE* 3.9 22.7 - - + -
196A LEU* 5.4 2.5 - - + -
208A VAL* 3.3 11.8 + - + +
211A THR* 1.3 80.6 - - - +
213A ARG* 1.3 51.4 + - - +
214A ARG 2.7 2.8 + - - -
215A TYR* 2.9 12.1 + - + -
216A GLY* 2.6 34.1 + - - -
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR* 4.8 9.0 - - - -
107A ASN* 3.0 32.2 + - - +
110A THR* 4.9 2.5 - - + -
209A TYR* 3.0 69.1 + - + +
210A GLU 4.0 2.7 - - - +
211A THR 3.0 1.6 + - - -
212A VAL* 1.3 77.9 - - - +
214A ARG* 1.3 57.0 + - - +
216A GLY* 4.0 2.1 - - - -
217A HIS* 3.1 41.1 + - - -
111B ILE* 5.7 1.6 - - - +
114B ARG* 5.6 12.1 - - - +
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Residues in contact with ARG 214 (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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210A GLU* 3.6 21.6 + - - +
211A THR* 2.6 30.4 + - - +
213A ARG* 1.3 73.8 - - - +
215A TYR* 1.3 53.8 + - - +
216A GLY 2.7 4.7 - - - -
217A HIS* 2.6 12.9 + - + +
218A GLU* 2.3 70.5 + - + +
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Residues in contact with TYR 215 (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 ARG* 4.3 23.5 + - - -
145A ASP* 4.1 8.7 + - - -
149A PHE* 4.5 3.8 - + - -
179A TYR* 4.3 5.5 + - - -
180A PHE* 5.0 1.4 - - - -
188A LEU* 3.7 33.4 - - + -
189A ALA* 3.2 32.5 - - - +
192A PHE* 3.1 54.2 - + + -
193A TYR* 5.2 0.2 + - - -
211A THR* 2.9 11.2 + - + +
212A VAL* 3.6 9.4 - - + +
214A ARG* 1.3 78.7 - - - +
216A GLY* 1.3 51.3 + - - +
218A GLU* 3.8 7.6 - - - +
219A SER* 2.5 56.8 + - - -
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Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 5.3 3.4 - - - -
106A THR* 4.4 21.5 - - - -
212A VAL 2.6 16.2 + - - -
213A ARG 4.6 1.8 - - - -
214A ARG 2.7 0.8 - - - -
215A TYR* 1.3 76.7 - - - +
217A HIS* 1.3 58.5 + - - -
219A SER* 3.5 2.6 + - - -
220A GLY* 3.0 24.6 + - - -
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Residues in contact with HIS 217 (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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213A ARG* 3.1 39.4 + - - -
214A ARG* 2.6 18.8 + - + +
216A GLY* 1.3 69.8 - - - +
218A GLU* 1.3 56.9 + - - +
220A GLY* 3.2 1.5 + - - -
221A GLU* 2.8 35.9 + - - +
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Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 3.5 33.3 - - + +
214A ARG* 2.3 75.6 + - + +
215A TYR* 3.9 6.5 - - - +
217A HIS* 1.3 69.2 - - - +
219A SER* 1.3 67.1 + - - +
221A GLU* 2.9 14.2 + - - +
222A ILE* 3.3 10.4 + - - +
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Residues in contact with SER 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 6.1 1.0 - - - +
105A ARG* 4.2 13.6 + - - -
179A TYR* 3.3 29.2 - - - -
188A LEU* 3.7 2.1 - - - +
215A TYR* 2.5 39.8 + - - -
216A GLY* 3.5 4.9 + - - -
218A GLU* 1.3 77.6 - - - +
220A GLY* 1.3 64.0 + - - +
222A ILE* 2.9 31.4 + - - +
223A TRP* 3.1 6.3 + - - +
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Residues in contact with GLY 220 (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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102A LEU* 5.7 8.1 - - - -
216A GLY 3.0 15.6 + - - -
217A HIS* 3.4 1.8 - - - -
218A GLU 2.9 2.4 + - - -
219A SER* 1.3 81.5 + - - +
221A GLU* 1.3 54.1 + - - -
223A TRP* 2.7 28.0 + - - +
224A HIS* 2.8 27.0 + - - -
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Residues in contact with GLU 221 (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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217A HIS 2.8 15.7 + - - +
218A GLU* 2.9 10.9 + - - +
220A GLY* 1.3 70.6 - - - -
222A ILE* 1.3 61.1 + - + +
224A HIS* 4.0 8.9 - - - +
225A ARG* 3.1 26.9 + - - +
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Residues in contact with ILE 222 (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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179A TYR* 3.9 11.9 - - + +
182A ASN* 4.4 16.4 - - - +
184A GLU* 4.5 22.4 - - + +
185A ALA* 3.9 31.6 - - + +
188A LEU* 3.6 31.0 - - + -
218A GLU 3.3 12.6 - - - +
219A SER* 2.9 13.9 - - - +
221A GLU* 1.3 76.0 - - + +
223A TRP* 1.3 60.7 + - - +
225A ARG* 3.4 5.5 + - - +
226A MET* 2.9 32.1 + - - +
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Residues in contact with TRP 223 (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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95A PRO* 6.2 2.2 - - - +
98A ILE* 4.4 22.6 - - + +
99A ASP* 5.1 6.0 + - - -
102A LEU* 4.8 18.2 - - + -
175A ILE* 4.3 18.6 - - + -
178A HIS* 4.1 17.7 - + + -
179A TYR* 3.3 55.2 - - + -
219A SER 3.1 6.4 + - - +
220A GLY* 2.7 16.1 + - - +
222A ILE* 1.3 68.4 - - - +
224A HIS* 1.3 69.4 + + - +
225A ARG 2.9 4.0 - - - -
226A MET* 2.4 42.3 + - + +
227A GLN* 3.0 23.6 + - + +
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Residues in contact with HIS 224 (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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99A ASP* 3.5 29.4 + - - -
220A GLY* 2.8 30.2 + - - +
221A GLU* 4.0 7.2 - - - +
223A TRP* 1.3 87.4 - + - +
225A ARG* 1.3 57.1 + - - +
227A GLN* 3.5 6.4 + - - +
228A LYS* 3.4 25.6 + - - +
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Residues in contact with ARG 225 (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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221A GLU 3.1 19.3 + - - +
222A ILE* 3.6 7.9 - - - +
223A TRP 2.8 1.4 + - - -
224A HIS* 1.3 77.4 - - - +
226A MET* 1.3 59.8 + - - +
227A GLN 3.4 0.7 - - - -
228A LYS* 4.3 9.2 - - - +
229A ASN* 4.1 9.7 + - - -
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Residues in contact with MET 226 (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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178A HIS 4.2 8.5 - - - +
179A TYR* 3.2 33.7 - - - +
181A ALA* 4.6 3.8 - - + -
182A ASN* 3.2 47.3 - - + +
222A ILE* 2.9 27.6 - - - +
223A TRP* 2.4 39.4 + - + +
225A ARG* 1.3 72.0 - - - +
227A GLN* 1.3 58.5 + - - +
228A LYS 3.6 0.2 - - - -
229A ASN* 4.0 13.9 + - - +
230A LEU* 4.9 5.5 - - - +
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Residues in contact with GLN 227 (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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223A TRP* 3.0 25.0 + - + +
224A HIS* 3.5 8.3 + - - +
226A MET* 1.3 81.5 - - - +
228A LYS* 1.3 49.9 + - - +
229A ASN* 2.4 22.2 + - - +
230A LEU* 3.0 22.2 + - - +
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Residues in contact with LYS 228 (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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224A HIS 3.4 16.0 + - - +
225A ARG* 4.7 7.2 - - - +
226A MET 3.6 1.2 - - - +
227A GLN* 1.3 72.5 - - - +
229A ASN* 1.3 70.8 + - - +
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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