Contacts of the helix formed by residues 168 - 182 (chain K) in PDB entry 5XTE
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 ASN 168 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 5.2 11.3 - - + -
29B LEU* 4.3 23.0 - - - +
40B GLN* 5.4 2.9 + - - -
47B ARG* 4.6 15.6 - - - +
49B PHE* 5.7 8.1 - - - -
164K VAL 5.2 0.4 + - - -
165K ALA 4.0 5.0 + - - +
166K PHE* 3.5 5.3 - - - +
167K GLN* 1.3 85.8 - - - +
169K PRO* 1.3 67.0 - - - +
170K GLN* 3.2 15.5 + - - +
171K THR* 2.7 41.8 + - + +
172K HIS 3.8 0.5 + - - -
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Residues in contact with PRO 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLN* 6.5 1.3 - - + -
41B PRO* 5.3 11.7 - - + -
166K PHE 4.5 3.1 - - - +
167K GLN 3.7 7.5 - - - +
168K ASN* 1.3 83.6 - - - +
170K GLN* 1.3 76.0 + - - +
172K HIS* 2.9 27.3 + - + +
173K VAL* 2.9 17.7 + - - +
264K ASP* 5.4 2.9 - - - +
268K HIS* 3.2 35.2 - - + +
441K SER* 5.5 1.3 - - - -
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Residues in contact with GLN 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 6.0 0.6 - - + -
27B ARG* 3.7 36.6 - - + -
28B PRO 3.4 20.9 + - - +
29B LEU* 3.8 13.2 - - - +
168K ASN* 3.4 14.6 - - - +
169K PRO* 1.3 97.9 - - + +
171K THR* 1.3 57.2 + - + +
173K VAL* 3.0 3.0 + - - +
174K ILE* 2.9 32.2 + - - +
268K HIS* 4.4 8.4 - - + -
339K TYR* 3.4 34.8 - - + +
341K ILE* 4.8 4.0 - - - +
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Residues in contact with THR 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.7 20.2 - - + -
27B ARG* 3.2 24.2 - - - +
165K ALA 2.9 23.6 + - - +
166K PHE* 3.2 13.8 - - - -
168K ASN* 2.7 25.0 + - + +
170K GLN* 1.3 76.1 - - + +
172K HIS* 1.3 58.7 + - - +
175K GLU* 2.7 48.0 + - - +
191K TYR* 4.9 8.5 - - - +
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Residues in contact with HIS 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K PHE* 4.1 38.7 - + + +
168K ASN 4.7 0.4 - - - +
169K PRO* 2.9 18.7 + - + +
171K THR* 1.3 81.7 + - - +
173K VAL* 1.3 56.5 + - - +
175K GLU 4.1 2.2 + - - +
176K ASN* 3.2 29.1 + - - +
260K GLU* 2.7 42.6 + - - -
262K ASN* 4.9 7.2 + - - -
441K SER* 3.3 13.7 - - - -
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Residues in contact with VAL 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K PRO 2.9 17.6 + - - +
170K GLN 3.0 6.7 + - - +
172K HIS* 1.3 79.1 - - - +
174K ILE* 1.3 59.5 + - + +
176K ASN* 3.4 4.7 - - - +
177K LEU* 2.9 24.2 + - + +
268K HIS* 3.7 22.0 - - + -
269K ALA 5.2 0.2 - - - -
270K ALA* 4.6 3.8 - - + -
339K TYR* 3.5 39.9 - - + +
439K ALA* 3.8 28.3 - - + +
440K ALA 4.9 0.4 - - - +
441K SER* 3.9 20.0 - - - +
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Residues in contact with ILE 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PRO* 4.4 5.6 - - + -
27B ARG* 3.2 55.9 - - + +
170K GLN 2.9 10.8 + - - +
173K VAL* 1.3 79.3 - - + +
175K GLU* 1.3 55.0 + - - +
176K ASN 2.6 17.4 + - - -
177K LEU* 2.9 22.7 + - + -
178K HIS* 3.0 39.5 + - + +
326K PHE* 3.6 33.9 - - + -
339K TYR* 4.8 12.8 - - + -
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Residues in contact with GLU 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PRO* 4.2 5.7 - - - +
11B PHE* 4.4 2.1 - - - +
27B ARG* 2.7 38.5 + - - -
116K ARG* 3.2 29.0 + - - +
166K PHE* 5.0 13.7 - - + -
171K THR* 2.7 37.3 + - - +
172K HIS* 4.1 4.0 + - - +
174K ILE* 1.3 70.8 - - - +
176K ASN* 1.3 62.3 + - - +
179K ALA* 5.6 0.7 - - - -
189K PRO* 5.2 11.4 - - + +
190K LEU* 3.5 36.1 - - + +
191K TYR* 5.0 12.3 + - + -
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Residues in contact with ASN 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172K HIS* 3.2 22.6 + - - +
173K VAL* 3.4 4.9 - - - +
174K ILE 2.6 2.2 + - - -
175K GLU* 1.3 76.9 - - - +
177K LEU* 1.3 62.9 + - - +
178K HIS 3.3 2.3 - - - +
179K ALA* 3.1 14.3 + - - +
180K ALA 2.9 20.4 + - - -
258K ILE* 3.1 37.1 + - - +
260K GLU* 2.3 34.4 + - - +
439K ALA* 4.6 4.0 - - - -
441K SER* 5.1 0.2 + - - -
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Residues in contact with LEU 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173K VAL 2.9 19.8 + - - +
174K ILE* 3.5 17.7 - - + +
176K ASN* 1.3 75.1 - - - +
178K HIS* 1.3 68.0 + - + +
180K ALA* 3.0 5.8 + - + +
181K ALA* 2.9 21.5 + - + +
270K ALA* 3.8 25.1 - - + +
272K VAL* 3.5 31.4 - - + -
326K PHE* 4.5 17.3 - - + -
335K LEU* 5.6 1.8 - - + -
339K TYR* 5.8 0.2 - - + -
437K SER* 4.5 2.5 - - - -
438K MET* 3.9 10.5 - - - +
439K ALA* 3.7 33.6 - - + +
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Residues in contact with HIS 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PRO* 4.7 2.9 - - + +
116K ARG* 3.3 31.7 + - - +
174K ILE* 3.0 40.9 + - + +
175K GLU 5.5 0.2 - - - -
176K ASN 4.9 0.7 - - - +
177K LEU* 1.3 81.0 - - + +
179K ALA* 1.3 64.5 + - - +
181K ALA* 2.9 16.9 + - - +
182K TYR* 3.1 26.0 + - + +
186K LEU* 3.9 16.2 + - - +
187K ALA* 4.0 3.3 - - - +
326K PHE* 4.5 10.1 - - - -
328K ALA* 4.8 1.3 - - + +
330K TYR* 3.1 44.9 + + - -
335K LEU* 4.5 15.5 - - + +
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Residues in contact with ALA 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175K GLU 5.6 0.4 - - - -
176K ASN* 3.1 20.5 + - - +
178K HIS* 1.3 80.2 - - - +
180K ALA* 1.3 61.0 + - - +
182K TYR 3.6 11.6 - - - +
187K ALA* 3.9 27.4 + - + +
189K PRO* 6.2 0.2 - - + -
254K ARG* 3.5 12.1 + - - -
258K ILE* 4.2 10.5 - - + +
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Residues in contact with ALA 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176K ASN 2.9 7.9 + - - +
177K LEU* 3.0 15.0 + - + +
179K ALA* 1.3 78.1 - - - +
181K ALA* 1.3 55.6 + - - +
182K TYR 3.7 0.2 - - - -
254K ARG* 3.1 29.3 + - - +
256K GLY 3.1 26.4 + - - +
258K ILE* 3.6 24.7 - - + -
437K SER* 3.4 2.6 + - - -
438K MET 3.8 15.5 - - - +
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Residues in contact with ALA 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177K LEU* 2.9 14.3 + - + +
178K HIS 2.9 4.4 + - - +
180K ALA* 1.3 78.8 - - - +
182K TYR* 1.3 58.0 + - + +
253K TYR* 3.2 19.3 - - + -
254K ARG* 2.4 33.8 + - - +
272K VAL* 5.0 1.6 - - + -
335K LEU* 4.1 25.8 - - + -
437K SER* 3.3 20.0 - - - +
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Residues in contact with TYR 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178K HIS* 3.1 21.9 + - - +
179K ALA 3.6 4.2 - - - +
181K ALA* 1.3 87.8 - - + +
183K ARG* 1.3 64.0 + - - +
184K ASN 4.2 3.4 - - - +
186K LEU* 3.4 39.9 - - + +
187K ALA* 3.3 27.7 - - + +
251K ALA* 3.9 15.0 - - + -
252K ASN 3.2 16.6 - - - +
253K TYR* 3.8 16.2 - + + -
254K ARG* 3.5 11.5 - - - +
274K GLU* 5.9 0.7 - - + -
330K TYR* 4.8 2.1 - + - -
333K SER* 3.3 34.2 + - - -
334K GLY 3.8 0.9 + - - -
335K LEU* 3.5 38.6 - - + +
449W PHE* 4.9 0.5 - - - -
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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
------------------------------------------------------------
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