Contacts of the helix formed by residues 198 - 214 (chain A) in PDB entry 4HI7
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 TYR 198 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.3 10.5 - - + -
165A ILE* 3.4 31.1 - - + +
169A SER* 4.1 5.4 - - - -
189A ILE* 5.0 1.6 - - - +
192A LEU* 3.3 33.2 - - + +
193A GLU* 3.5 41.6 + - + +
195A LEU* 3.1 21.4 + - + +
196A PRO 3.4 1.4 + - - -
197A TYR* 1.3 77.3 - - - +
199A ALA* 1.3 57.1 + - - +
201A ASN* 2.8 53.2 + - + +
202A SER* 3.0 33.2 + - - -
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Residues in contact with ALA 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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196A PRO 5.0 2.5 + - - +
197A TYR 3.0 2.4 + - - -
198A TYR* 1.3 76.2 - - - +
200A GLU* 1.3 61.4 + - - +
201A ASN 3.0 1.5 + - - -
202A SER* 3.3 15.9 - - - +
203A THR* 3.2 33.4 + - - +
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Residues in contact with GLU 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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10A ASP* 5.0 5.7 - - - +
16A ARG* 3.5 19.6 - - - +
19A LYS* 3.1 60.4 - - + +
20A LEU* 4.3 9.2 - - + -
23A ALA* 4.5 11.0 - - + -
29A TYR* 4.9 3.4 + - - +
197A TYR* 3.0 17.1 + - + +
199A ALA* 1.3 78.0 - - - +
201A ASN* 1.3 56.4 + - - +
203A THR* 5.0 0.7 - - - -
204A GLY 5.2 1.7 + - - -
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Residues in contact with ASN 201 (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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16A ARG* 2.9 38.7 + - - +
20A LEU* 3.9 24.6 - - + +
165A ILE* 4.1 4.2 + - - +
166A SER* 3.6 10.9 - - - -
169A SER* 3.0 24.6 + - - -
198A TYR* 2.8 37.6 + - + +
200A GLU* 1.3 80.3 - - - +
202A SER* 1.3 60.6 + - - +
203A THR 3.3 2.4 + - - -
204A GLY 4.2 0.2 - - - -
205A ALA* 2.9 26.7 + - - +
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 3.0 29.9 + - - -
199A ALA* 3.3 20.6 + - - +
201A ASN* 1.3 77.4 - - - +
203A THR* 1.3 66.0 + - - +
205A ALA* 3.8 6.8 - - - +
206A GLN* 2.9 40.5 + - - +
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Residues in contact with THR 203 (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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10A ASP* 4.7 11.4 - - - +
199A ALA* 3.2 25.0 + - - +
200A GLU 5.6 0.2 - - - -
202A SER* 1.3 80.6 + - - +
204A GLY* 1.3 61.7 + - - +
206A GLN* 3.4 8.2 + - - +
207A GLN* 3.1 40.4 + - + +
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Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 3.2 25.1 - - - +
11A ALA* 3.6 4.9 - - - -
16A ARG* 3.5 10.2 - - - +
200A GLU 5.2 1.4 + - - -
201A ASN 3.5 3.6 + - - -
202A SER 3.4 0.2 - - - -
203A THR* 1.3 77.8 - - - +
205A ALA* 1.3 59.9 + - - +
207A GLN* 3.2 16.1 + - - +
208A PHE* 2.9 28.2 + - - +
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Residues in contact with ALA 205 (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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16A ARG* 3.5 22.9 - - - +
169A SER* 3.7 28.6 - - - +
201A ASN 2.9 19.3 + - - +
202A SER* 3.8 7.6 - - - +
204A GLY* 1.3 74.4 - - - +
206A GLN* 1.3 59.4 + - + +
208A PHE* 3.1 4.0 + - - +
209A VAL* 2.9 34.6 + - + +
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Residues in contact with GLN 206 (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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202A SER* 2.9 33.2 + - - +
203A THR* 3.7 6.9 - - - +
205A ALA* 1.3 76.8 - - + +
207A GLN* 1.3 56.7 + - + +
209A VAL* 3.4 9.0 + - + +
210A ALA* 2.9 28.8 + - - +
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Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 5.9 0.7 - - - +
10A ASP* 3.6 26.6 + - - +
11A ALA* 3.8 15.4 + - + +
203A THR* 3.1 28.3 + - + +
204A GLY* 3.2 8.7 + - - +
206A GLN* 1.3 76.0 - - + +
208A PHE* 1.3 58.3 + - - +
210A ALA* 3.3 6.8 + - - +
211A ALA* 2.9 30.0 + - - +
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Residues in contact with PHE 208 (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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11A ALA* 3.6 26.4 - - + +
13A PRO* 4.5 6.3 - - + -
16A ARG* 4.0 5.8 - - - +
112A LEU* 4.2 14.6 - - + -
116A ALA* 3.9 29.2 - - + -
120A LEU* 4.3 12.3 - - + -
170A SER* 3.4 44.9 - - - +
173A ALA* 4.1 0.9 - - + -
174A PHE* 3.9 12.8 - + - -
204A GLY 2.9 13.6 + - - +
205A ALA* 3.1 8.5 + - - +
207A GLN* 1.3 76.5 - - - +
209A VAL* 1.3 64.8 - - - +
211A ALA* 3.1 7.7 + - - +
212A VAL* 3.0 39.4 + - + +
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Residues in contact with VAL 209 (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 SER 4.3 11.7 - - - +
170A SER 4.8 0.7 - - - +
172A VAL* 4.5 6.1 - - + -
173A ALA* 3.9 31.6 - - + +
205A ALA 2.9 21.9 + - - +
206A GLN* 3.7 8.3 - - - +
208A PHE* 1.3 76.6 - - + +
210A ALA* 1.3 56.7 + - - +
212A VAL* 3.3 3.5 + - - +
213A LYS* 2.9 49.3 + - + +
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Residues in contact with ALA 210 (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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206A GLN 2.9 18.3 + - - +
207A GLN* 3.6 7.0 - - - +
209A VAL* 1.3 74.6 - - - +
211A ALA* 1.3 65.9 + - - +
213A LYS* 3.4 7.7 + - - +
214A SER* 3.0 24.3 + - - -
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Residues in contact with ALA 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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37A MET* 5.5 7.0 - - + -
120A LEU* 3.5 29.6 - - + +
207A GLN 2.9 13.4 + - - +
208A PHE* 3.1 11.6 + - - +
210A ALA* 1.3 75.1 - - - +
212A VAL* 1.3 60.3 + - - +
214A SER* 2.7 24.6 + - - -
215A LYS* 3.5 4.2 + - - +
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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
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119A ILE* 4.9 3.1 - - + -
120A LEU* 4.0 17.0 - - + -
173A ALA* 3.9 20.0 - - + +
174A PHE* 3.6 36.3 - - + -
208A PHE* 3.0 43.5 + - + +
209A VAL 3.6 7.0 - - - +
211A ALA* 1.3 72.7 - - - +
213A LYS* 1.3 68.6 + - + +
214A SER 3.1 1.8 - - - -
215A LYS 3.0 23.0 + - - +
216A PRO* 4.9 0.3 - - - +
217A PHE* 4.2 12.5 - - + -
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Residues in contact with LYS 213 (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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172A VAL 5.1 1.0 + - - -
173A ALA* 2.9 27.7 + - - +
209A VAL* 2.9 37.1 + - + +
210A ALA* 3.4 7.1 + - - +
212A VAL* 1.3 78.7 - - + +
214A SER* 1.3 59.4 + - - +
215A LYS 3.2 1.2 + - - -
216A PRO* 4.2 9.9 - - - +
217A PHE* 6.3 0.2 - - - -
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Residues in contact with SER 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 ALA 3.0 13.3 + - - -
211A ALA* 2.7 22.9 + - - -
213A LYS* 1.3 77.0 - - - +
215A LYS* 1.3 68.8 + - - +
216A PRO* 3.4 9.9 - - - +
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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