Contacts of the helix formed by residues 195 - 207 (chain D) in PDB entry 1SXG
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 LYS 195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D ILE* 3.6 38.4 - - + -
160D ASP* 5.4 3.6 + - - +
161D TYR* 3.8 22.2 - - + +
162D GLU* 3.1 37.5 - - + +
190D PRO 3.4 3.0 + - - +
191D ILE* 3.1 11.7 - - - +
192D ASN 3.2 3.4 + - - -
193D HIS 3.6 0.2 - - - -
194D ALA* 1.3 89.8 - - - +
196D LYS* 1.3 63.9 + - - +
197D VAL 3.6 0.2 - - - -
198D LYS* 4.0 2.0 - - - -
199D GLY* 3.0 21.1 + - - -
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Residues in contact with LYS 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161D TYR* 4.4 6.7 - - + +
165D ALA* 3.6 23.7 - - + +
182D PHE* 4.0 16.8 - - + -
191D ILE* 2.8 44.6 + - + +
192D ASN* 3.9 22.7 - - - +
195D LYS* 1.3 70.4 - - - +
197D VAL* 1.3 67.7 + - - +
199D GLY 3.2 1.9 + - - -
200D TYR* 2.9 22.9 + - - +
221D TYR* 5.5 3.4 - - - -
244D PHE* 5.0 1.1 - - + -
246D GLY* 3.0 36.5 + - - +
247D THR* 4.8 6.1 - - - +
274D PHE* 3.6 34.2 - - + -
275D ASP* 5.0 1.6 + - - -
292D GLN* 5.2 0.6 - - - +
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D PHE* 3.4 28.9 - - + -
184D SER* 4.2 0.9 - - - +
187D LEU* 3.9 25.1 - - + -
192D ASN* 2.8 34.9 + - + +
193D HIS* 3.8 10.8 - - - +
196D LYS* 1.3 71.9 - - - +
198D LYS* 1.3 68.0 + - - +
200D TYR* 3.1 5.2 + - - +
201D LYS* 3.1 42.7 + - - +
216D ILE* 4.3 14.1 - - + -
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Residues in contact with LYS 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D GLU* 4.5 8.3 - - + +
192D ASN 4.0 1.6 + - - -
193D HIS 3.1 26.1 + - - +
194D ALA* 4.1 21.5 - - - +
195D LYS 3.7 8.3 + - - +
197D VAL* 1.3 79.1 - - - +
199D GLY* 1.3 58.4 + - - +
201D LYS* 2.8 43.5 + - - +
202D ARG* 2.9 12.3 + - + +
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Residues in contact with GLY 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D GLU* 3.0 38.5 + - - -
166D PHE* 3.6 20.5 - - - -
195D LYS 3.0 8.1 + - - -
196D LYS 3.7 2.7 - - - -
198D LYS* 1.3 78.8 - - - +
200D TYR* 1.3 56.3 + - - +
201D LYS 3.2 0.2 - - - -
202D ARG* 3.7 2.0 - - - -
203D ALA* 3.1 22.5 + - - +
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Residues in contact with TYR 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ALA* 4.6 1.7 - - - +
169D VAL* 3.8 26.4 - - + +
180D ILE* 2.4 38.6 + - + -
181D ALA* 3.3 20.9 - - - -
182D PHE* 3.7 29.0 + + + -
196D LYS 2.9 12.7 + - - +
197D VAL* 3.4 12.8 - - - +
198D LYS 3.0 0.2 + - - -
199D GLY* 1.3 76.8 - - - +
201D LYS* 1.3 66.8 + - + +
203D ALA* 4.2 1.7 - - - +
204D LEU* 3.4 41.5 + - + +
211D VAL* 5.1 2.2 - - + -
212D ARG 5.7 0.7 + - - -
215D TYR* 3.7 9.9 + - - +
216D ILE* 3.7 30.1 - - + -
244D PHE* 4.8 10.8 - + + -
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Residues in contact with LYS 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D VAL* 3.1 23.5 + - - +
198D LYS* 2.8 27.9 + - - +
200D TYR* 1.3 85.4 - - + +
202D ARG* 1.3 60.2 + - - +
204D LEU* 3.5 4.6 + - - +
205D THR* 2.8 37.5 + - + +
211D VAL* 3.6 27.8 - - + -
213D ASP* 5.5 5.0 + - - -
216D ILE* 3.8 23.3 - - - +
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Residues in contact with ARG 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D GLU* 3.0 32.5 + - - -
163D GLN* 2.8 32.3 - - - +
166D PHE* 3.3 22.2 - - + -
198D LYS* 2.9 12.6 + - + +
199D GLY* 3.8 7.9 - - - +
200D TYR 3.3 0.2 - - - -
201D LYS* 1.3 76.6 - - - +
203D ALA* 1.3 58.5 + - - +
205D THR* 3.8 5.2 - - - +
206D GLU* 2.7 76.9 + - + +
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Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE* 3.5 28.2 - - + +
169D VAL* 3.2 38.8 - - + -
170D GLN* 4.1 13.6 + - - +
173D ILE* 4.3 3.6 - - + +
199D GLY 3.1 8.5 + - - +
202D ARG* 1.3 76.4 - - - +
204D LEU* 1.3 63.2 + - - +
206D GLU* 4.1 0.7 - - - +
207D SER* 3.2 27.0 + - - -
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 4.0 16.4 - - + -
173D ILE* 3.9 9.2 - - + -
178D LYS 4.8 2.2 - - - +
180D ILE* 4.2 15.9 - - + +
200D TYR* 3.4 42.1 + - + +
201D LYS 3.6 4.7 - - - +
202D ARG 3.2 0.4 - - - -
203D ALA* 1.3 81.4 - - - +
205D THR* 1.3 61.0 + - - +
207D SER 3.3 1.2 + - - -
208D GLY 3.1 4.5 + - - -
209D LEU* 2.7 60.8 + - + +
210D PRO 4.4 4.5 - - - +
211D VAL* 4.0 31.9 - - + -
212D ARG 5.1 0.7 - - - +
215D TYR* 6.0 0.9 - - + -
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Residues in contact with THR 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D LYS* 2.8 30.5 + - + +
202D ARG* 3.3 7.6 + - - +
204D LEU* 1.3 68.0 - - - +
206D GLU* 1.3 62.5 + - - +
207D SER 2.9 4.9 - - - -
208D GLY* 2.6 25.8 + - - +
209D LEU 4.3 6.3 - - - +
211D VAL* 3.6 22.0 - - + -
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Residues in contact with GLU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE* 3.6 14.7 - - + -
170D GLN* 6.3 0.2 - - - +
202D ARG* 2.7 72.9 + - + +
203D ALA* 4.3 3.8 - - - +
205D THR* 1.3 76.3 + - - +
207D SER* 1.3 57.0 + - - +
208D GLY 3.3 0.4 - - - -
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Residues in contact with SER 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D GLN* 5.0 5.2 - - - -
173D ILE* 3.1 32.8 - - - +
203D ALA 3.2 18.4 + - - -
204D LEU 3.5 2.7 - - - -
205D THR 2.9 1.0 - - - -
206D GLU* 1.3 77.7 - - - +
208D GLY* 1.3 64.4 + - - +
209D LEU* 3.9 11.0 - - - +
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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