Contacts of the helix formed by residues 187 - 201 (chain t) in PDB entry 6QX2
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 187 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100t ARG* 3.4 5.3 - - - +
101t TYR* 3.7 1.8 - - - -
186t HIS* 1.3 72.2 - - - +
188t LEU* 1.3 62.1 + - - +
189t THR* 3.2 34.7 + - - -
190t GLU* 3.3 30.9 + - + +
191t LEU* 3.0 29.6 + - - +
215t GLY 4.9 2.4 + - - -
217t ASP* 3.0 34.3 + - + +
482t ASP* 2.9 23.4 + - - +
483t ASP 3.3 14.1 + - - -
484t ARG* 3.4 5.7 - - - +
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Residues in contact with LEU 188 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101t TYR* 2.9 31.8 + - + +
131t ILE* 4.1 16.2 - - + -
164t PHE* 3.9 23.8 - - + -
165t PRO* 4.0 15.3 - - + -
169t ALA* 4.5 7.2 - - + -
186t HIS 3.7 0.6 + - - -
187t ASN* 1.3 69.5 + - - +
189t THR* 1.3 59.6 + - - +
191t LEU* 3.2 7.4 + - + +
192t ILE* 2.9 52.7 + - + +
476t ILE* 4.6 5.6 - - + -
477t ARG* 5.4 0.2 - - - -
480t PHE* 3.8 36.1 - - + +
481t GLY* 4.1 5.8 - - - +
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Residues in contact with THR 189 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187t ASN* 3.2 10.6 + - - -
188t LEU* 1.3 78.4 - - - +
190t GLU* 1.3 64.1 + - + +
192t ILE* 3.3 1.9 + - - +
193t ASN* 3.0 42.1 + - - +
477t ARG* 3.9 22.2 + - + +
481t GLY* 3.1 24.0 - - - -
482t ASP 3.2 12.3 + - - -
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Residues in contact with GLU 190 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186t HIS* 6.4 0.2 - - + -
187t ASN* 3.3 24.8 + - + +
189t THR* 1.3 77.2 - - + +
191t LEU* 1.3 57.5 + - - +
193t ASN* 3.4 8.8 + - - +
194t GLY 2.9 24.1 + - - -
212t ASP* 3.2 24.4 - - - +
213t ILE* 3.6 15.4 - - + +
214t GLU* 3.1 29.7 + - - +
215t GLY 4.0 2.3 - - - +
484t ARG* 2.8 50.4 + - - +
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Residues in contact with LEU 191 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165t PRO* 3.7 24.5 - - + +
168t LEU* 3.7 28.3 - - + -
169t ALA* 3.4 42.0 - - + +
186t HIS* 3.8 16.6 - - + -
187t ASN 3.0 16.5 + - - +
188t LEU* 3.4 11.2 - - - +
190t GLU* 1.3 76.1 - - + +
192t ILE* 1.3 56.4 + - - +
194t GLY* 3.0 5.4 + - - -
195t VAL* 2.9 32.0 + - - +
213t ILE* 3.9 24.5 - - + +
352t LEU* 4.6 4.7 - - + +
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Residues in contact with ILE 192 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165t PRO* 4.2 13.0 - - + -
188t LEU* 2.9 35.1 + - + +
189t THR 4.0 2.7 - - - +
191t LEU* 1.3 72.2 - - - +
193t ASN* 1.3 59.8 + - - +
195t VAL* 3.1 9.1 + - - +
196t LEU* 2.9 41.9 + - + +
473t LEU* 3.6 44.0 - - + +
474t THR 4.6 0.2 - - - +
476t ILE* 3.9 15.7 - - + -
477t ARG* 3.7 40.6 - - + +
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Residues in contact with ASN 193 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189t THR* 3.0 33.0 + - - +
190t GLU* 3.6 9.4 - - - +
192t ILE* 1.3 74.5 - - - +
194t GLY* 1.3 56.2 + - - +
196t LEU* 3.4 7.8 + - - +
197t SER* 3.0 33.4 + - - -
212t ASP* 3.6 21.3 + - + +
477t ARG* 2.7 34.8 + - - +
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Residues in contact with GLY 194 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190t GLU 2.9 14.9 + - - -
191t LEU 3.0 6.5 + - - -
193t ASN* 1.3 75.7 - - - +
195t VAL* 1.3 54.6 + - - +
197t SER* 3.3 4.3 + - - -
198t LEU* 3.0 25.1 + - - +
209t LEU* 3.5 19.3 - - - +
212t ASP* 3.6 15.8 - - - +
213t ILE* 4.4 9.0 - - - -
352t LEU* 4.5 3.1 - - - -
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Residues in contact with VAL 195 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165t PRO* 4.7 6.1 - - + -
191t LEU 2.9 20.2 + - - +
192t ILE* 3.1 9.4 + - - +
194t GLY* 1.3 71.7 - - - +
196t LEU* 1.3 55.9 + - - +
198t LEU* 3.3 9.9 + - + +
199t SER* 2.8 32.9 + - - -
352t LEU* 3.7 26.0 - - + +
355t TYR* 4.2 22.0 - - + -
356t LEU* 3.9 27.3 - - + +
473t LEU* 3.7 27.1 - - + -
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Residues in contact with LEU 196 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192t ILE* 2.9 30.5 + - + +
193t ASN* 3.6 6.7 - - - +
195t VAL* 1.3 72.3 - - - +
197t SER* 1.3 63.6 + - - +
199t SER* 2.8 21.4 + - - -
200t LYS* 3.2 20.5 + - + +
470t ARG* 3.7 47.6 - - + +
473t LEU* 4.6 10.8 - - + -
474t THR* 3.7 17.0 - - - +
477t ARG* 3.7 22.4 - - - +
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Residues in contact with SER 197 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193t ASN 3.0 8.6 + - - -
194t GLY 3.3 7.2 + - - -
196t LEU* 1.3 74.7 - - - +
198t LEU* 1.3 61.5 + - - +
200t LYS* 3.2 12.0 + - - +
201t ASN* 3.1 22.5 + - - +
204t ILE* 3.8 21.2 - - - +
209t LEU* 4.8 0.2 - - - -
212t ASP* 2.7 31.3 + - - -
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Residues in contact with LEU 198 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194t GLY 3.0 13.6 + - - +
195t VAL* 3.5 9.2 - - - +
197t SER* 1.3 74.8 - - - +
199t SER* 1.3 57.5 + - - +
200t LYS 3.1 0.2 - - - -
201t ASN 3.1 31.5 + - - +
202t PRO* 3.4 11.1 - - + +
204t ILE* 3.6 27.9 - - + +
209t LEU* 4.5 5.4 - - + -
349t LYS* 4.0 11.9 - - + +
352t LEU* 3.7 19.1 - - + +
353t VAL* 3.7 48.9 - - + +
356t LEU* 4.1 17.6 - - + +
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Residues in contact with SER 199 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195t VAL* 2.8 19.7 + - - -
196t LEU* 2.8 16.8 + - - -
198t LEU* 1.3 72.2 - - - +
200t LYS* 1.3 53.4 + - - +
202t PRO* 5.3 2.9 - - - +
356t LEU* 3.7 28.9 - - - -
466t LEU* 3.5 17.0 - - - +
469t VAL* 6.4 0.2 - - - -
470t ARG* 2.9 50.9 + - - +
473t LEU* 6.5 0.2 - - - -
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Residues in contact with LYS 200 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196t LEU* 3.2 20.3 + - + +
197t SER* 3.6 10.1 - - - +
198t LEU 3.1 0.6 - - - -
199t SER* 1.3 77.2 - - - +
201t ASN* 1.3 58.5 + - + +
202t PRO* 4.0 6.5 - - - +
470t ARG* 3.7 27.6 - - - +
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Residues in contact with ASN 201 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197t SER 3.1 9.4 + - - +
198t LEU* 3.1 10.1 + - - +
200t LYS* 1.3 79.5 - - + +
202t PRO* 1.3 67.2 - - - +
203t ASP* 3.0 21.2 + - - +
204t ILE* 3.1 45.4 + - + +
208t GLU* 4.3 11.1 + - - -
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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