Contacts of the helix formed by residues 205 - 219 (chain A) in PDB entry 1U9C
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.5 1.1 - - - -
188A THR 3.6 0.5 + - - -
189A ASP* 3.4 10.3 - - - -
190A PHE 3.0 38.0 + - - -
200A GLY* 4.0 4.7 - - - -
201A GLN 3.4 9.5 + - - -
202A ASN* 2.8 27.6 + - - -
204A GLN* 1.3 76.9 - - - +
206A SER* 1.3 59.5 + - - +
207A ARG 3.4 1.8 - - - -
208A SER* 3.3 3.6 + - - -
209A THR* 2.7 33.6 + - - -
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Residues in contact with SER 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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26A GLU* 3.9 19.5 + - - +
27A GLU* 3.3 30.8 + - - +
30A VAL* 4.2 7.2 - - - -
31A PRO* 3.8 15.1 - - - +
125A VAL* 4.3 8.6 - - - +
202A ASN 3.8 1.3 + - - -
203A PRO* 2.8 21.6 + - - +
204A GLN 3.4 1.2 - - - -
205A SER* 1.3 76.8 - - - +
207A ARG* 1.3 63.7 + - - +
209A THR* 3.4 3.1 + - - -
210A ALA* 3.1 23.4 + - - +
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Residues in contact with ARG 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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30A VAL* 3.7 38.0 - - + +
33A LEU* 5.3 12.9 - - - +
34A VAL* 3.9 18.6 - - + +
37A GLU* 5.0 6.3 + - - -
63A ASP* 5.7 2.8 + - - -
66A TRP* 5.8 0.6 - - - +
204A GLN 5.0 3.0 + - - +
205A SER 3.4 0.2 - - - -
206A SER* 1.3 79.3 - - - +
208A SER* 1.3 57.6 + - - +
210A ALA* 3.2 5.4 + - - +
211A GLU* 2.9 48.8 + - + +
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Residues in contact with SER 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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189A ASP* 2.6 38.7 + - - -
191A SER* 2.8 23.5 + - - -
205A SER 3.3 6.6 + - - -
206A SER 3.4 0.2 - - - -
207A ARG* 1.3 78.3 - - - +
209A THR* 1.3 63.6 + - - +
211A GLU* 3.3 8.4 + - - +
212A LYS* 3.0 31.9 + - - +
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Residues in contact with THR 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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91A PHE* 3.9 22.7 - - + -
123A ALA* 4.5 1.3 - - + -
124A ALA 4.1 20.9 - - - +
125A VAL* 4.4 3.0 - - + +
191A SER* 3.5 8.4 - - - -
198A ILE* 3.8 21.7 - - + +
199A THR 4.2 0.2 - - - -
200A GLY* 3.3 23.0 - - - +
205A SER 2.7 22.9 + - - -
206A SER* 3.7 5.2 - - - -
208A SER* 1.3 77.4 + - - +
210A ALA* 1.3 62.5 - - - +
212A LYS* 3.2 6.5 + - - +
213A VAL* 3.2 20.1 + - - +
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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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31A PRO* 3.8 30.7 - - + -
34A VAL* 4.1 17.7 - - + -
35A PHE* 3.7 8.9 - - + -
91A PHE* 4.1 9.3 - - - -
206A SER 3.1 13.6 + - - +
207A ARG* 3.2 7.6 + - - +
209A THR* 1.3 78.4 - - - +
211A GLU* 1.3 56.3 + - - +
213A VAL* 3.1 5.5 + - - +
214A VAL* 3.0 29.7 + - - +
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Residues in contact with GLU 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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34A VAL* 3.7 27.4 - - + +
37A GLU* 5.6 0.7 - - - +
207A ARG* 2.9 35.1 + - + +
208A SER* 3.8 7.6 - - - +
209A THR 3.2 0.2 - - - -
210A ALA* 1.3 76.1 - - - +
212A LYS* 1.3 58.1 + - - +
214A VAL* 3.4 19.7 + - - +
215A ALA* 3.0 27.5 + - - +
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Residues in contact with LYS 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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191A SER* 2.8 46.0 + - - +
192A VAL* 3.9 17.9 - - - +
193A ARG* 3.8 24.2 + - + +
198A ILE* 3.6 21.7 - - + +
208A SER* 3.0 17.9 + - - +
209A THR 3.2 8.2 + - - +
211A GLU* 1.3 74.8 - - - +
213A VAL* 1.3 59.6 + - - +
215A ALA* 3.3 6.3 + - - +
216A ALA* 3.0 29.1 + - - +
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Residues in contact with VAL 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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5A VAL* 5.2 1.3 - - + -
35A PHE* 3.8 21.1 - - + -
89A ALA* 4.0 17.9 - - + -
91A PHE* 4.2 9.4 - - + -
121A ILE* 4.3 5.6 - - + -
123A ALA* 3.5 31.9 - - + -
198A ILE* 4.0 14.6 - - + -
209A THR 3.2 12.2 + - - +
210A ALA 3.1 8.2 + - - +
212A LYS* 1.3 72.3 - - - +
214A VAL* 1.3 66.4 + - - +
216A ALA* 3.2 3.9 + - - +
217A LEU* 2.9 38.7 + - + +
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Residues in contact with VAL 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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34A VAL* 3.7 25.4 - - + -
35A PHE* 4.2 3.8 - - + -
38A LYS* 3.8 24.9 - - + -
40A TYR* 3.7 26.4 + - + +
210A ALA 3.0 18.3 + - - +
211A GLU* 3.6 18.2 - - - +
213A VAL* 1.3 75.1 - - - +
215A ALA* 1.3 57.8 + - - +
217A LEU* 3.2 2.6 + - - +
218A GLU* 2.8 55.1 + - - +
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Residues in contact with ALA 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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193A ARG* 4.7 4.3 - - - +
211A GLU 3.0 17.9 + - - +
212A LYS* 3.6 7.2 - - - +
214A VAL* 1.3 76.9 - - - +
216A ALA* 1.3 63.2 + - - +
218A GLU* 3.2 17.9 + - - +
219A GLU* 3.2 33.2 + - - +
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Residues in contact with ALA 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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121A ILE* 3.6 26.7 - - + -
193A ARG* 3.8 28.9 - - - +
195A GLY 5.5 0.7 - - - +
196A ASN* 6.3 0.4 - - - -
198A ILE* 4.4 8.3 - - + -
212A LYS 3.0 17.3 + - - +
213A VAL 3.2 2.0 + - - +
215A ALA* 1.3 76.0 - - - +
217A LEU* 1.3 59.9 + - - +
219A GLU* 3.4 13.0 + - - +
220A ARG* 3.3 24.8 + - - +
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Residues in contact with LEU 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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3A LYS* 3.8 18.5 - - + -
5A VAL* 4.2 14.1 - - + -
40A TYR* 3.6 40.4 - - + +
88A ASP* 3.5 31.9 - - + +
89A ALA* 4.5 1.1 - - + -
121A ILE* 3.4 22.4 - - + -
213A VAL* 2.9 32.7 + - + +
214A VAL 3.7 0.2 - - - +
216A ALA* 1.3 72.5 - - - +
218A GLU* 1.3 64.5 + - - +
220A ARG* 3.0 20.2 + - - +
221A GLU* 2.8 17.8 + - - +
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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
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38A LYS* 3.0 29.2 + - - +
40A TYR* 4.6 4.5 - - - +
214A VAL* 2.8 32.6 + - + +
215A ALA* 3.4 17.7 - - - +
217A LEU* 1.3 77.5 - - - +
219A GLU* 1.3 61.3 + - + +
220A ARG 3.2 0.7 + - - -
221A GLU* 3.3 28.1 + - + +
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Residues in contact with GLU 219 (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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193A ARG* 2.8 44.5 + - - -
215A ALA* 3.2 17.9 + - - +
216A ALA* 3.4 7.8 - - - +
217A LEU 3.2 0.2 - - - -
218A GLU* 1.3 75.8 - - + +
220A ARG* 1.3 64.7 + - + +
221A GLU 3.4 5.5 + - - +
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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