Contacts of the helix formed by residues 202 - 214 (chain C) in PDB entry 4L28
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 SER 202 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C THR* 3.9 0.9 - - - -
192C PRO 5.4 0.4 - - - -
195C ALA* 4.1 11.4 - - - -
196C ARG 3.2 24.0 - - - -
197C PHE* 3.1 27.2 + - - -
199C SER* 3.2 6.7 + - - -
200C PRO 3.3 1.0 - - - -
201C GLU* 1.3 80.3 - - - +
203C HIS* 1.3 64.6 + - - +
204C VAL* 3.7 4.3 + - - +
205C GLY 3.0 14.0 + - - -
206C VAL* 2.8 27.5 + - - +
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Residues in contact with HIS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C PRO* 3.6 22.6 - - + +
146C THR 3.7 19.7 - - - -
168C VAL* 3.4 24.2 - - + +
170C PRO* 4.3 17.2 - - + +
191C THR* 3.5 27.2 + - - +
197C PHE* 5.9 2.9 - - + -
202C SER* 1.3 76.8 - - - +
204C VAL* 1.3 72.2 + - + +
207C ALA* 3.0 28.9 + - - +
223C TYR* 3.0 23.9 + + - -
308C TYR* 4.1 17.9 + + - -
309C ASP* 6.1 0.4 - - - -
310C PHE* 5.0 5.6 - + - -
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Residues in contact with VAL 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 3.9 13.5 - - + +
46C PRO* 4.2 26.0 - - + -
145C PRO* 4.1 10.8 - - + -
197C PHE* 5.1 6.3 - - + +
202C SER* 3.2 5.7 - - - +
203C HIS* 1.3 98.1 + - + +
205C GLY* 1.3 66.9 + - - +
207C ALA* 3.2 2.1 + - - +
208C TRP* 3.0 48.4 + - + +
221C ASP* 5.8 2.2 - - - +
223C TYR* 4.1 21.5 - - + -
310C PHE* 4.9 5.4 - - + -
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Residues in contact with GLY 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 4.5 11.9 - - - -
197C PHE 5.0 1.1 + - - -
199C SER 4.4 4.5 - - - -
200C PRO* 3.9 13.5 - - - -
202C SER* 3.0 15.3 + - - -
204C VAL* 1.3 80.8 - - - +
206C VAL* 1.3 58.1 + - - +
208C TRP* 3.2 4.9 + - - +
209C ARG* 2.9 33.2 + - - +
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A HIS* 4.4 9.9 - - + +
537A ILE* 4.4 12.1 - - + -
168C VAL* 4.1 5.2 - - + -
189C VAL* 4.0 26.9 - - + -
191C THR* 3.6 19.7 - - + -
200C PRO 3.5 2.0 + - - +
201C GLU* 3.7 5.8 - - - +
202C SER 2.8 20.3 + - - +
203C HIS 4.1 1.6 - - - +
205C GLY* 1.3 74.8 - - - +
207C ALA* 1.3 64.4 + - - +
209C ARG* 3.4 29.1 - - - +
210C LEU* 2.9 32.9 + - + +
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Residues in contact with ALA 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE* 3.9 19.1 - - + +
145C PRO* 3.7 29.4 - - + -
168C VAL* 4.2 8.0 - - + +
203C HIS 3.0 19.5 + - - +
204C VAL 3.4 6.3 - - - +
205C GLY 3.1 0.2 - - - -
206C VAL* 1.3 78.3 - - - +
208C TRP* 1.3 57.7 + - + +
210C LEU* 3.2 4.4 + - - +
211C LYS* 2.9 23.2 + - - +
219C ILE* 3.6 12.9 - - + +
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Residues in contact with TRP 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 3.4 39.3 - + + -
44C ILE* 3.6 58.4 + - + -
145C PRO* 6.3 0.4 - - + -
204C VAL* 3.0 35.3 + - + +
205C GLY 3.7 5.4 - - - +
207C ALA* 1.3 76.4 - - + +
209C ARG* 1.3 64.4 + - + +
211C LYS* 3.1 27.7 + - + +
212C ASN* 3.0 37.5 + - - +
219C ILE* 3.6 30.6 - - + +
221C ASP* 3.9 21.4 + - + -
224C ARG* 4.7 3.8 - - - -
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Residues in contact with ARG 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A HIS* 4.8 5.1 + - - -
537A ILE* 3.5 37.3 - - + +
200C PRO* 2.4 52.6 + - - +
201C GLU* 3.8 7.7 + - - +
205C GLY* 2.9 17.8 + - - +
206C VAL* 3.4 18.1 - - - +
208C TRP* 1.3 78.2 - - + +
210C LEU* 1.3 62.6 + - - +
212C ASN* 3.6 11.9 + - - +
213C GLU* 3.5 22.0 - - - +
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Residues in contact with LEU 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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536A ALA* 5.3 3.1 - - + +
537A ILE* 4.2 20.6 - - + +
540A LEU* 3.9 26.5 - - + -
143C ILE* 4.0 12.1 - - + -
166C ILE* 4.1 18.6 - - + -
168C VAL* 3.8 27.1 - - + -
189C VAL* 4.1 15.3 - - + -
206C VAL* 2.9 30.9 + - + +
207C ALA* 3.5 4.7 - - - +
209C ARG* 1.3 75.3 - - - +
211C LYS* 1.3 65.8 + - - +
213C GLU* 3.1 11.3 + - - +
214C ILE* 3.2 23.7 + - + +
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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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143C ILE* 3.7 5.8 - - + -
207C ALA 2.9 13.8 + - - +
208C TRP* 3.1 29.0 + - + +
210C LEU* 1.3 77.3 - - - +
212C ASN* 1.3 76.5 + - - +
214C ILE 3.3 8.0 - - - +
217C SER* 3.1 49.1 + - - +
218C HIS* 4.7 3.0 + - - +
219C ILE* 3.7 30.4 - - + +
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Residues in contact with ASN 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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43C TRP* 5.4 7.7 - - - +
208C TRP* 3.0 29.9 + - - +
209C ARG* 4.0 10.4 - - - +
210C LEU 3.1 0.6 - - - -
211C LYS* 1.3 95.5 - - - +
213C GLU* 1.3 68.1 + - - +
214C ILE 3.8 1.1 + - - +
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Residues in contact with GLU 213 (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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537A ILE* 5.6 5.4 - - + -
540A LEU* 3.7 26.7 - - + +
541A ASN* 3.5 23.1 - - - +
544A ALA* 5.5 10.0 - - - +
209C ARG 3.5 15.0 - - - +
210C LEU 3.1 4.2 + - - +
212C ASN* 1.3 84.4 - - - +
214C ILE* 1.3 62.4 + - - +
215C PRO* 3.5 9.6 - - - +
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Residues in contact with ILE 214 (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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540A LEU* 4.1 28.0 - - + -
141C THR* 4.5 4.5 - - - +
143C ILE* 4.2 8.5 - - + -
164C ARG* 4.0 22.9 - - - +
166C ILE* 3.9 27.4 - - + -
210C LEU* 3.2 22.6 + - + +
211C LYS 3.3 6.1 + - - +
212C ASN 5.2 0.7 - - - -
213C GLU* 1.3 81.7 - - - +
215C PRO* 1.3 76.4 - - + +
217C SER* 2.5 37.7 + - - +
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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