Contacts of the helix formed by residues 204 - 216 (chain A) in PDB entry 3H1I
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 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLU* 3.1 12.2 + - - -
203A ILE* 1.3 73.4 - - - +
205A HIS* 1.3 70.3 + - - +
206A LYS* 3.8 6.6 + - - +
207A GLU* 3.0 30.4 + - - +
208A LEU* 3.0 19.6 + - - +
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Residues in contact with HIS 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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15A ASN* 3.5 55.3 - - + +
16A VAL 4.2 0.2 + - - -
17A THR* 3.8 28.8 + - + +
25A VAL* 3.9 23.1 - - + -
26A ALA* 4.4 2.4 - - - -
27A SER* 3.6 24.7 + - - +
29A GLU* 3.3 11.7 + - + +
203A ILE 3.4 2.6 + - - -
204A SER* 1.3 72.2 + - - +
206A LYS* 1.3 70.7 + - + +
208A LEU* 3.0 7.7 + - - +
209A VAL* 3.0 24.1 + - + +
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Residues in contact with LYS 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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204A SER* 3.3 6.9 + - - +
205A HIS* 1.3 82.7 - - + +
207A GLU* 1.3 62.6 + - - +
209A VAL* 2.6 35.0 - - + +
210A ASP* 2.6 32.7 + - - +
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Residues in contact with GLU 207 (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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106A MET* 4.1 19.9 - - - +
107A PRO* 4.5 13.5 - - - +
204A SER* 3.0 29.0 + - - +
206A LYS* 1.3 81.2 - - - +
208A LEU* 1.3 65.4 + - - +
210A ASP* 3.1 24.2 + - + +
211A ALA* 3.2 7.6 + - - +
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Residues in contact with LEU 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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25A VAL* 3.8 22.7 - - + -
26A ALA 4.3 2.0 - - - +
27A SER* 3.7 25.6 - - - +
37A VAL* 5.4 1.6 - - + -
106A MET* 3.2 34.5 - - + -
110A VAL* 3.9 5.8 - - + -
197A LEU* 3.7 24.7 - - + +
199A ALA* 3.7 24.9 - - + -
203A ILE* 4.2 6.3 - - + -
204A SER 3.0 9.8 + - - +
205A HIS* 3.1 8.7 - - - +
207A GLU* 1.3 76.1 - - - +
209A VAL* 1.3 66.4 + - - +
210A ASP 2.7 1.9 + - - -
211A ALA* 3.0 5.7 + - - +
212A ALA* 2.9 19.6 + - - +
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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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17A THR* 3.7 24.9 - - + +
19A LEU* 4.5 15.0 - - + -
25A VAL* 4.4 12.8 - - + +
205A HIS* 3.0 11.3 + - + +
206A LYS* 2.6 45.1 - - + +
208A LEU* 1.3 79.8 - - - +
210A ASP* 1.3 56.9 + - - +
212A ALA* 2.8 9.9 - - - +
213A ARG* 2.8 49.7 + - - +
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Residues in contact with ASP 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 LYS* 2.6 52.4 + - - +
207A GLU* 3.1 12.0 - - + +
208A LEU 2.7 4.8 + - - -
209A VAL* 1.3 71.7 - - - +
211A ALA* 1.3 55.7 + - - +
212A ALA 2.7 14.3 + - - -
213A ARG* 2.7 30.6 + - - +
214A GLN* 2.9 13.3 + - - +
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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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106A MET* 4.8 1.6 - - + -
107A PRO* 4.3 29.6 - - + -
110A VAL* 4.0 17.3 - - + +
207A GLU 3.2 6.3 + - - +
208A LEU 3.0 9.4 + - - +
210A ASP* 1.3 76.3 - - - +
212A ALA* 1.3 59.3 + - - +
214A GLN* 3.6 13.9 - - - +
215A HIS* 2.9 38.3 + - + +
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Residues in contact with ALA 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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19A LEU* 4.5 4.7 - - + -
25A VAL* 3.9 22.4 - - + -
110A VAL* 4.4 3.5 - - - +
197A LEU* 4.1 10.3 - - + -
208A LEU 2.9 8.1 + - - +
209A VAL* 2.8 25.6 - - + +
210A ASP 2.7 0.8 + - - -
211A ALA* 1.3 74.3 - - - +
213A ARG* 1.3 64.1 + - - +
214A GLN 2.9 1.3 + - - -
216A PHE* 2.9 44.4 + - + +
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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
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18A THR 5.7 1.4 + - - -
19A LEU* 4.0 33.2 - - + +
20A ASP* 5.7 3.0 + - - -
209A VAL* 2.8 37.7 + - + +
210A ASP* 2.7 23.9 + - - +
212A ALA* 1.3 73.3 - - - +
214A GLN* 1.3 61.3 + - - +
215A HIS 3.8 0.2 + - - -
216A PHE 4.4 0.3 - - - -
217A SER* 4.2 16.3 + - - -
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Residues in contact with GLN 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 ASP 2.9 11.8 + - - +
211A ALA* 3.5 15.1 - - - +
212A ALA 2.9 1.2 - - - -
213A ARG* 1.3 79.9 - - - +
215A HIS* 1.3 76.8 + - + +
217A SER* 4.5 8.7 + - - -
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Residues in contact with HIS 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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69A LYS* 5.9 1.3 - - - -
107A PRO 5.1 2.9 - - - -
110A VAL* 4.9 2.0 - - + +
111A GLU* 3.3 51.6 + - + +
114A ALA* 3.9 19.2 - - + +
118A GLN* 3.8 18.0 + - - -
211A ALA* 2.9 34.9 + - + +
214A GLN* 1.3 100.8 + - + +
216A PHE* 1.3 60.2 + - + +
217A SER* 3.1 15.0 + - - -
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Residues in contact with PHE 216 (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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19A LEU* 3.9 14.7 - - + +
21A ASN* 4.0 6.1 + - - +
23A LEU* 3.3 35.4 - - + -
39A VAL* 5.0 10.5 - - + -
110A VAL* 4.1 10.5 - - + -
113A LEU* 4.4 4.0 - - + -
114A ALA* 3.0 44.4 - - + -
117A VAL* 4.3 12.1 - - + -
118A GLN* 4.0 15.3 - - - -
195A MET* 6.4 1.6 - - + -
197A LEU* 3.6 39.0 - - + -
212A ALA* 2.9 29.1 + - - +
213A ARG 4.4 1.5 - - - +
215A HIS* 1.3 73.8 - - - +
217A SER* 1.3 57.4 + - - +
218A GLY 2.9 9.0 + - - -
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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