Contacts of the helix formed by residues 195 - 207 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148P ILE* 4.2 25.7 - - + +
152P ASN* 6.0 1.8 - - - +
160P ASP* 5.5 4.4 + - - +
161P TYR* 3.6 27.6 - - + +
162P GLU* 3.4 32.2 - - + +
190P PRO* 3.1 12.4 + - + +
191P ILE* 3.7 7.2 - - - +
192P ASN 3.6 0.6 + - - -
194P ALA* 1.3 93.6 - - + +
196P LYS* 1.3 62.0 + - - +
197P VAL 3.5 0.9 - - - -
198P LYS* 3.6 1.7 + - - +
199P GLY 3.0 23.2 + - - -
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Residues in contact with LYS 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161P TYR* 4.3 17.4 - - + +
165P ALA* 3.4 18.6 - - + +
182P PHE* 4.2 13.0 - - + -
191P ILE* 3.0 37.5 + - - +
192P ASN* 3.6 25.7 - - - +
195P LYS* 1.3 72.6 - - - +
197P VAL* 1.3 70.2 + - - +
199P GLY 3.1 1.0 + - - -
200P TYR* 3.1 20.3 + - - +
221P TYR* 5.5 4.6 - - - -
244P PHE* 5.3 0.7 - - + -
246P GLY* 2.9 37.6 + - - +
247P THR* 4.6 3.8 + - - -
274P PHE* 4.1 31.5 - - + -
275P ASP* 5.0 3.2 + - - -
292P GLN* 5.8 0.2 - - - +
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Residues in contact with VAL 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182P PHE* 4.2 22.9 - - + -
187P LEU* 3.6 25.6 - - + -
192P ASN* 2.6 41.3 + - + +
193P HIS* 3.6 10.8 - - - +
196P LYS* 1.3 73.9 - - - +
198P LYS* 1.3 65.5 + - + +
200P TYR* 3.2 5.2 + - + +
201P LYS* 3.0 44.1 + - + +
216P ILE* 4.9 12.6 - - + -
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Residues in contact with LYS 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P GLU* 4.1 8.1 - - + +
192P ASN 4.4 0.2 + - - -
193P HIS 4.6 5.3 + - - +
194P ALA 4.3 15.0 - - - +
195P LYS 3.6 6.5 + - - +
196P LYS 3.3 0.6 - - - -
197P VAL* 1.3 76.9 - - + +
199P GLY* 1.3 60.6 + - - +
201P LYS* 3.5 35.3 - - + +
202P ARG* 2.8 42.4 + - + +
205P THR* 5.6 2.4 + - - -
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Residues in contact with GLY 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P GLU* 3.4 37.4 + - - -
165P ALA* 4.0 1.3 - - - -
166P PHE* 3.6 18.7 - - - -
195P LYS 3.0 12.8 + - - -
196P LYS 3.1 3.5 + - - -
198P LYS* 1.3 75.9 - - - +
200P TYR* 1.3 63.0 + - - +
203P ALA* 3.0 19.1 + - - +
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Residues in contact with TYR 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P ALA* 4.0 2.0 - - - +
169P VAL* 3.7 31.4 - - + -
180P ILE* 2.6 36.7 + - + -
181P ALA* 3.8 4.3 - - - -
182P PHE* 3.7 38.6 - + + -
196P LYS 3.1 10.7 + - - +
197P VAL* 3.4 11.9 - - + +
199P GLY* 1.3 73.8 - - - +
201P LYS* 1.3 83.3 + - + +
203P ALA* 3.2 11.1 + - - +
204P LEU* 3.3 33.5 + - + +
211P VAL* 5.1 1.7 - - + +
212P ARG* 4.9 1.0 + - - +
215P TYR* 3.5 19.6 - - - +
216P ILE* 3.5 31.9 - - + +
244P PHE* 4.6 2.2 - + + -
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Residues in contact with LYS 201 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197P VAL* 3.0 30.9 + - + +
198P LYS* 3.5 41.3 - - + +
200P TYR* 1.3 89.3 - - + +
202P ARG* 1.3 57.6 + - - +
204P LEU* 3.2 3.1 + - - +
205P THR* 2.8 33.0 + - - +
211P VAL* 3.4 40.9 - - + +
213P ASP* 4.6 10.9 + - - -
216P ILE* 4.9 9.1 - - - +
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Residues in contact with ARG 202 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P GLU* 2.5 40.6 + - - +
163P GLN* 3.0 24.0 + - - +
166P PHE* 3.1 29.1 - - - -
198P LYS* 2.8 31.7 + - + +
199P GLY 3.8 3.4 - - - +
201P LYS* 1.3 71.7 - - - +
203P ALA* 1.3 59.1 + - - +
205P THR* 4.0 9.0 - - + -
206P GLU* 2.9 49.6 + - + +
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Residues in contact with ALA 203 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P PHE* 3.3 30.2 - - + +
169P VAL* 3.5 34.3 - - + -
170P GLN* 4.1 2.8 - - - +
173P ILE* 3.5 9.2 - - + +
199P GLY 3.0 14.2 + - - +
200P TYR 3.2 0.6 + - - +
202P ARG* 1.3 76.6 - - - +
204P LEU* 1.3 65.8 + - - +
206P GLU* 3.5 2.9 + - - +
207P SER* 3.2 22.5 + - - -
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Residues in contact with LEU 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169P VAL* 4.5 6.3 - - + -
173P ILE* 4.5 2.5 - - + -
178P LYS 4.4 4.7 - - - +
180P ILE* 4.2 23.8 - - + +
200P TYR* 3.3 45.7 + - + +
201P LYS 3.2 6.2 + - - +
203P ALA* 1.3 76.9 - - - +
205P THR* 1.3 69.8 + - - +
207P SER* 2.6 15.8 + - - -
208P GLY 3.3 5.9 + - - -
209P LEU* 3.3 40.1 + - + -
210P PRO 3.5 22.2 - - - +
211P VAL* 3.9 13.7 - - + -
212P ARG* 5.7 0.4 - - - +
215P TYR* 6.1 0.7 - - + -
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Residues in contact with THR 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198P LYS* 5.6 2.4 + - - -
201P LYS* 2.8 30.7 + - - +
202P ARG* 3.7 11.2 - - + -
204P LEU* 1.3 74.8 - - - +
206P GLU* 1.3 60.1 + - + +
208P GLY* 2.9 19.2 + - - -
209P LEU 3.9 8.8 + - - +
211P VAL* 3.9 11.6 - - - +
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Residues in contact with GLU 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P PHE* 3.3 33.1 - - + -
170P GLN* 5.5 1.5 - - - +
202P ARG* 2.9 38.2 + - + +
203P ALA 3.7 4.7 - - - +
204P LEU 3.0 0.2 + - - -
205P THR* 1.3 77.8 - - + +
207P SER* 1.3 58.8 + - - +
208P GLY 3.3 0.2 - - - -
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Residues in contact with SER 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170P GLN* 3.8 10.2 + - - -
173P ILE* 3.4 33.8 - - - +
203P ALA 3.2 11.2 + - - -
204P LEU 2.6 16.8 + - - -
206P GLU* 1.3 74.9 - - - +
208P GLY* 1.3 56.4 + - - -
209P LEU* 3.1 15.6 + - - +
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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