Contacts of the helix formed by residues 181 - 196 (chain K) in PDB entry 3V3K
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 GLY 181 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179K ARG 3.6 0.2 + - - -
180K THR* 1.3 72.8 - - - +
182K SER* 1.3 62.6 + - - +
183K ASN* 3.3 7.5 - - - +
184K ILE* 3.3 23.8 + - - +
185K ASP* 3.6 3.2 + - - +
341K ARG* 4.9 1.8 - - - -
343K PRO* 3.7 21.8 + - - -
346K GLY* 3.4 25.0 - - - -
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Residues in contact with SER 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K ASN* 2.7 27.1 + - - +
171K VAL* 3.8 4.5 - - - -
179K ARG* 2.7 53.8 + - - -
180K THR 3.3 1.0 + - - -
181K GLY* 1.3 76.0 - - - +
183K ASN* 1.3 59.6 + - - +
185K ASP* 3.2 13.4 + - - +
186K CYS* 2.9 26.5 + - - +
235K LEU* 3.6 6.1 - - - +
341K ARG* 4.5 3.0 - - - +
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Residues in contact with ASN 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K ASN* 3.3 21.0 + - - +
171K VAL* 3.6 21.0 - - - +
172K ASN* 6.0 0.8 - - - +
179K ARG 4.9 0.2 + - - -
180K THR* 6.2 0.6 - - - +
181K GLY* 3.3 5.0 - - - +
182K SER* 1.3 75.2 - - - +
184K ILE* 1.3 64.0 + - + +
186K CYS* 3.5 1.5 + - - +
187K GLU* 3.2 31.5 + - + +
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Residues in contact with ILE 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181K GLY* 3.3 14.5 + - - +
182K SER 3.2 0.4 - - - -
183K ASN* 1.3 76.8 - - + +
185K ASP* 1.3 57.9 + - - +
187K GLU* 3.9 2.6 - - - +
188K LYS* 3.0 47.2 + - + +
343K PRO 4.1 10.3 - - - +
344K LYS 3.2 30.5 - - - +
345K SER* 3.2 25.6 - - - +
346K GLY 4.2 0.2 - - - +
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Residues in contact with ASP 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179K ARG* 5.2 1.2 + - - -
181K GLY 3.6 8.9 + - - +
182K SER* 3.2 16.5 + - - +
184K ILE* 1.3 75.4 - - - +
186K CYS* 1.3 59.8 + - - +
188K LYS* 3.3 5.7 + - - +
189K LEU* 2.9 35.2 + - - +
235K LEU* 3.8 13.8 - - + +
283K GLN* 5.1 2.1 - - - +
341K ARG* 5.4 0.7 - - - -
345K SER 4.5 2.1 - - - +
346K GLY* 3.7 5.7 - - - -
347K SER* 3.0 40.7 + - - +
350K VAL* 3.4 34.2 - - + +
351K GLU* 4.3 2.8 + - - -
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Residues in contact with CYS 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ILE* 4.4 8.7 - - - +
169K ASN* 3.4 35.7 - - - +
182K SER 2.9 8.7 + - - +
183K ASN* 3.7 6.1 - - - +
184K ILE 3.4 0.2 - - - -
185K ASP* 1.3 77.7 - - - +
187K GLU* 1.3 62.4 - - - +
189K LEU* 3.4 3.9 + - - +
190K ARG* 2.8 34.9 + - - +
202K VAL* 3.4 42.0 - - - -
235K LEU* 3.8 7.8 - - + +
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Residues in contact with GLU 187 (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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183K ASN* 3.2 18.2 + - + +
184K ILE* 4.3 2.9 - - - +
186K CYS* 1.3 84.7 - - + +
188K LYS* 1.3 63.2 + - - +
190K ARG* 3.4 40.4 + - - +
191K ARG* 3.4 32.7 + - - +
202K VAL* 5.5 0.7 - - - +
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Residues in contact with LYS 188 (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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184K ILE* 3.0 40.0 + - + +
185K ASP* 3.5 11.2 + - - +
186K CYS 3.3 0.2 - - - -
187K GLU* 1.3 78.1 - - - +
189K LEU* 1.3 57.3 + - - +
191K ARG* 3.7 5.4 + - - +
192K ARG* 3.2 24.9 + - - +
345K SER* 4.3 9.3 + - - -
350K VAL* 4.9 3.6 - - + +
351K GLU* 3.6 40.9 + - - +
354K ASP* 3.6 38.1 - - + +
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Residues in contact with LEU 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ILE* 4.3 8.1 - - + -
185K ASP 2.9 20.4 + - - +
186K CYS* 3.9 3.4 - - - +
188K LYS* 1.3 75.1 - - - +
190K ARG* 1.3 60.6 + - - +
192K ARG* 4.0 9.2 - - + -
193K PHE* 2.9 59.4 + - + +
233K VAL* 3.6 31.4 - - + -
235K LEU* 4.3 11.9 - - + -
281K PHE* 6.1 1.6 - - + -
350K VAL* 3.9 25.1 - - + -
353K LEU* 4.5 24.7 - - + -
354K ASP* 5.3 6.3 - - + -
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Residues in contact with ARG 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167K ILE* 4.2 2.2 - - - +
186K CYS 2.8 21.2 + - - +
187K GLU* 3.4 37.6 + - - +
189K LEU* 1.3 73.6 - - - +
191K ARG* 1.3 61.7 + - + +
194K SER* 3.2 22.7 + - - -
200K VAL* 3.7 29.5 + - + +
201K GLU* 6.0 1.0 - - - +
202K VAL* 3.7 34.9 + - + +
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Residues in contact with ARG 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K GLU* 3.4 22.1 + - - +
188K LYS* 4.0 4.5 - - - +
189K LEU 3.3 0.4 - - - -
190K ARG* 1.3 79.5 - - + +
192K ARG* 1.3 54.2 + - - +
194K SER* 3.5 4.9 + - - -
195K SER* 2.8 34.7 + - - -
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Residues in contact with ARG 192 (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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188K LYS 3.2 17.4 + - - +
189K LEU* 3.1 16.2 + - + +
191K ARG* 1.3 76.3 - - - +
193K PHE* 1.3 61.7 + - + +
195K SER* 3.2 19.6 + - - -
196K LEU* 3.0 36.0 + - + +
353K LEU* 5.7 0.7 - - + -
354K ASP* 2.8 34.9 + - - +
357K PHE* 3.9 35.9 + - + -
358K GLU* 3.2 56.8 + - - +
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Residues in contact with PHE 193 (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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165K CYS* 3.7 29.8 - - - -
167K ILE* 4.6 1.6 - - + -
189K LEU* 2.9 51.3 + - + +
192K ARG* 1.3 73.2 - - + +
194K SER* 1.3 60.6 + - - +
196K LEU* 3.1 33.7 + - + +
197K HIS 3.2 0.7 + - - -
198K PHE* 3.0 31.6 + + + +
200K VAL* 3.8 8.1 - - + -
231K VAL* 3.8 31.2 - - + -
233K VAL* 3.7 20.6 - - + -
281K PHE* 3.9 24.5 - + - -
353K LEU* 5.5 2.0 - - + -
357K PHE* 4.9 7.9 - + - -
400K PHE* 4.8 7.0 - + - -
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Residues in contact with SER 194 (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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190K ARG 3.2 18.2 + - - -
191K ARG* 3.7 5.8 - - - -
192K ARG 3.3 0.2 - - - -
193K PHE* 1.3 77.2 - - - +
195K SER* 1.3 61.0 + - - +
197K HIS* 3.2 15.4 + - - -
198K PHE 3.8 14.6 + - - +
200K VAL* 3.4 12.9 - - - +
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Residues in contact with SER 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191K ARG 2.8 15.8 + - - -
192K ARG* 3.2 27.8 + - - -
194K SER* 1.3 75.6 - - - +
196K LEU* 1.3 58.3 + - - +
197K HIS* 3.2 19.7 + - - -
401K LYS 4.2 1.7 - - - +
402K THR* 4.7 8.0 - - - +
403K SER 5.0 1.0 + - - -
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Residues in contact with LEU 196 (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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162K CYS* 4.2 3.8 + - - -
192K ARG* 3.0 23.8 + - + +
193K PHE* 3.1 24.8 + - + +
195K SER* 1.3 76.4 - - - +
197K HIS* 1.3 68.3 + - - +
198K PHE* 3.2 19.9 - - + -
357K PHE* 4.1 23.1 - - + -
361K ALA* 4.7 9.2 - - + -
400K PHE* 3.6 39.9 - - + -
401K LYS* 3.5 13.1 + - - +
402K THR* 3.4 30.1 - - + -
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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