Contacts of the helix formed by residues 192 - 212 (chain C) in PDB entry 3TMP
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 ASP 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A HIS* 5.0 0.2 - - - -
11B LYS* 6.0 2.2 - - - -
190C ALA 3.7 2.8 + - - +
191C MET* 1.3 72.6 - - - +
193C PRO* 1.3 72.5 - - + +
194C ALA* 4.5 3.6 - - + +
195C THR* 2.9 47.8 + - - +
196C VAL* 3.0 14.1 + - - +
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Residues in contact with PRO 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A PRO* 4.3 15.5 - - + -
313A THR* 3.7 28.5 - - + +
315A HIS* 3.7 36.1 - - + +
320A ASN* 6.1 0.2 - - - +
191C MET 3.5 8.0 - - - +
192C ASP* 1.3 84.7 - - + +
194C ALA* 1.3 64.3 + - - +
195C THR 3.1 0.2 + - - -
196C VAL* 3.3 9.8 + - + +
197C GLU* 2.9 24.8 + - - +
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Residues in contact with ALA 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ASP* 3.3 4.3 - - + +
193C PRO* 1.3 79.2 - - - +
195C THR* 1.3 59.7 + - - +
197C GLU* 3.4 18.7 - - - +
198C GLN* 3.1 25.0 + - - +
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Residues in contact with THR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C MET* 4.8 6.5 - - - -
192C ASP* 2.9 38.2 + - - +
194C ALA* 1.3 78.0 - - - +
196C VAL* 1.3 65.0 + - - +
197C GLU 3.2 0.7 - - - -
198C GLN* 3.2 21.6 + - - +
199C GLN* 3.1 42.5 + - - +
53H GLY* 6.2 3.4 - - - -
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A GLN* 4.9 5.4 - - - +
188C ILE* 4.1 8.5 - - + +
191C MET* 3.3 42.6 - - + +
192C ASP 3.0 15.0 + - - +
193C PRO* 3.6 9.2 - - + +
195C THR* 1.3 73.8 - - - +
197C GLU* 1.3 58.3 + - - +
199C GLN* 3.2 5.4 + - - +
200C GLU* 2.9 44.0 + - + +
331C ARG* 4.0 29.2 - - + -
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Residues in contact with GLU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A GLN* 5.9 2.7 - - - +
193C PRO 2.9 17.0 + - - +
194C ALA* 3.4 20.8 - - - +
195C THR 3.2 0.2 - - - -
196C VAL* 1.3 75.8 - - - +
198C GLN* 1.3 56.9 + - - +
200C GLU* 3.8 6.2 - - - +
201C HIS* 3.0 69.4 + - + +
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Residues in contact with GLN 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ALA 3.1 13.5 + - - +
195C THR* 3.2 26.9 + - - +
197C GLU* 1.3 80.8 - - - +
199C GLN* 1.3 59.8 + - + +
201C HIS* 3.5 6.6 + - - +
202C TRP* 3.1 26.7 + - - +
20H SER 5.5 2.9 - - - +
22H THR* 3.6 31.8 - - + +
53H GLY* 4.1 13.7 + - - +
55H THR* 4.1 13.2 - - - +
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Residues in contact with GLN 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C ARG* 2.9 33.0 + - - +
191C MET* 3.2 15.0 - - - +
195C THR* 3.1 34.6 + - - +
196C VAL* 3.6 6.1 - - - +
198C GLN* 1.3 81.2 - - + +
200C GLU* 1.3 60.9 + - + +
202C TRP* 3.3 6.9 + - - +
203C PHE* 2.9 31.5 + - - +
301C TYR* 3.4 41.2 - - + +
24H GLU* 3.7 15.7 + - - +
25H ASN* 6.0 0.2 - - - +
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Residues in contact with GLU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A GLN* 4.6 11.2 - - - +
196C VAL* 2.9 30.3 + - + +
197C GLU* 3.8 7.4 - - - +
199C GLN* 1.3 75.8 - - + +
201C HIS* 1.3 65.7 + - + +
203C PHE* 3.2 9.7 + - - +
204C GLU* 2.8 42.8 + - - +
301C TYR* 6.2 1.1 - - - -
330C HIS* 2.9 47.9 + - - +
331C ARG* 4.2 17.8 + - - +
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Residues in contact with HIS 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C GLU* 3.0 53.0 + - + +
198C GLN* 3.8 6.5 - - - +
199C GLN 3.3 0.2 - - - -
200C GLU* 1.3 80.0 - - + +
202C TRP* 1.3 65.0 + - - +
204C GLU* 3.5 14.6 + - - +
205C LYS* 3.1 25.1 + - - +
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Residues in contact with TRP 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C GLN 3.1 17.5 + - - +
199C GLN* 3.7 6.3 - - - +
201C HIS* 1.3 76.0 - - - +
203C PHE* 1.3 68.1 + + - +
205C LYS* 3.9 4.9 - - + +
206C ALA* 2.9 46.8 + - + +
210C LYS* 4.4 3.4 - - - -
301C TYR* 3.7 29.2 - + + -
302C SER 5.9 0.4 - - - -
305C THR 4.5 3.8 - - - -
306C SER* 3.3 51.1 - - - -
307C ALA 4.6 1.3 - - - -
308C VAL* 4.2 9.2 - - + -
21H ASP* 3.9 18.1 + - - -
25H ASN* 3.8 37.3 - - + +
29H LYS* 4.6 6.8 - - - +
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Residues in contact with PHE 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C GLN 2.9 17.5 + - - +
200C GLU* 3.6 10.5 - - - +
202C TRP* 1.3 86.6 - + + +
204C GLU* 1.3 66.2 + - + +
206C ALA* 3.9 0.9 - - - +
207C LEU* 3.0 53.1 + - + +
215C ILE* 4.7 3.4 - - + -
299C TYR* 3.9 10.5 - + + -
300C GLN* 3.6 25.8 - - - -
301C TYR* 3.5 41.5 - + + -
308C VAL* 4.1 22.7 - - + -
328C SER* 4.3 15.5 - - - -
329C TYR 5.7 1.3 - - - -
330C HIS* 4.4 16.8 - + - -
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Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C GLU* 2.8 30.4 + - - +
201C HIS* 3.9 16.3 + - - +
203C PHE* 1.3 79.9 - - + +
205C LYS* 1.3 61.8 + - - +
207C LEU* 3.4 5.6 + - - +
208C ARG* 3.1 24.4 + - - +
213C PHE 4.8 1.2 - - - +
215C ILE* 4.1 32.3 - - + +
217C GLN* 5.5 5.0 + - - -
330C HIS* 5.9 2.9 - - + -
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Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C HIS 3.1 17.6 + - - +
202C TRP* 3.9 4.5 - - + +
204C GLU* 1.3 74.7 - - - +
206C ALA* 1.3 60.5 + - - +
208C ARG* 3.2 32.4 + - - +
209C ASP* 2.8 65.3 + - - +
18H GLU* 5.1 17.1 + - - +
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Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C TRP* 2.9 36.6 + - + +
203C PHE 3.9 1.1 - - - +
205C LYS* 1.3 73.7 - - - +
207C LEU* 1.3 58.3 + - - +
209C ASP* 4.5 4.7 - - - -
210C LYS* 2.8 56.5 + - - +
308C VAL* 3.6 25.3 - - + +
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Residues in contact with LEU 207 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C PHE* 3.0 45.5 + - + +
204C GLU* 3.7 5.2 - - - +
205C LYS 3.2 0.2 - - - -
206C ALA* 1.3 75.0 - - - +
208C ARG* 1.3 58.2 - - - +
211C LYS* 3.0 26.4 + - + +
213C PHE* 3.2 46.9 + - + +
215C ILE* 3.3 36.1 - - + -
299C TYR* 4.1 17.0 - - + -
308C VAL* 4.0 22.4 - - + -
338C VAL* 4.7 5.2 - - + -
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Residues in contact with ARG 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C GLU 3.1 12.9 + - - +
205C LYS* 3.2 41.0 + - - +
207C LEU* 1.3 78.2 - - - +
209C ASP* 1.3 76.9 + - - +
212C GLY* 2.9 28.6 + - - -
213C PHE 3.5 12.9 + - - +
214C ILE* 4.3 22.2 - - + -
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Residues in contact with ASP 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C LYS* 2.8 54.4 + - - +
206C ALA* 4.0 5.0 - - - +
208C ARG* 1.3 94.3 + - - +
210C LYS* 1.3 64.8 + - + +
212C GLY 5.0 0.2 + - - -
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Residues in contact with LYS 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C TRP* 4.4 5.1 - - - -
206C ALA* 2.8 37.4 + - - +
209C ASP* 1.3 80.7 - - + +
211C LYS* 1.3 65.5 + - + +
306C SER* 3.1 29.6 + - - +
307C ALA* 4.8 3.6 - - + +
308C VAL* 4.0 22.9 - - + +
29H LYS* 5.6 2.0 - - - +
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Residues in contact with LYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C LEU* 3.0 18.8 + - + +
210C LYS* 1.3 83.5 - - + +
212C GLY* 1.3 63.1 + - - +
213C PHE* 3.4 41.5 - - + -
299C TYR* 4.3 7.3 + - + -
308C VAL* 2.9 48.7 - - + +
309C GLU* 3.3 33.6 + - - +
310C PRO* 4.9 0.8 - - - +
340C ASN* 5.0 1.6 - - - +
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Residues in contact with GLY 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C LEU 4.0 0.2 - - - -
208C ARG* 2.9 22.5 + - - -
209C ASP 5.0 0.4 + - - -
210C LYS 3.8 0.6 - - - -
211C LYS* 1.3 78.3 - - - +
213C PHE* 1.3 62.1 + - - +
214C ILE* 4.5 1.8 - - - +
340C ASN* 4.6 1.8 - - - +
341C PRO* 3.1 28.1 - - - +
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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