Contacts of the helix formed by residues 185 - 194 (chain D) in PDB entry 2G4C
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 LEU 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D ALA* 5.4 2.0 - - - -
182D ARG* 3.3 42.8 - - - +
184D ASN* 1.3 74.4 - - - +
186D LEU* 1.3 63.6 + - - +
187D HIS 3.4 1.1 - - - -
188D GLY* 3.4 5.2 + - - +
189D ALA* 3.3 17.7 + - - +
210D GLN* 3.7 51.8 + - + +
212D GLY* 3.7 11.7 - - - +
214D CYS* 4.1 10.3 - - - -
236D GLU* 3.3 30.3 - - + +
238D SER* 3.9 19.5 + - - +
339D ASN* 4.7 3.8 - - - +
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Residues in contact with LEU 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ASN* 3.3 16.9 + - + +
185D LEU* 1.3 74.6 - - - +
187D HIS* 1.3 66.1 + - - +
189D ALA* 3.1 13.2 + - - +
190D LEU* 3.2 22.5 + - + +
238D SER* 4.9 2.2 + - - -
240D VAL* 3.4 30.3 - - + -
282D GLU* 5.7 2.7 - - - +
306D LEU* 3.4 30.3 - - + -
310D GLU* 4.6 10.1 - - + -
335D VAL* 5.6 1.6 - - + -
337D SER* 3.1 35.7 - - - +
339D ASN* 5.5 1.7 - - - +
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Residues in contact with HIS 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D LYS* 4.0 23.7 - - + +
184D ASN* 3.4 12.6 + - - +
185D LEU 3.4 0.2 - - - -
186D LEU* 1.3 79.6 - - - +
188D GLY* 1.3 63.8 + - - +
189D ALA 3.1 1.0 + - - -
190D LEU* 3.3 9.4 + - - +
191D GLU* 3.0 54.7 + - - +
314D MET* 4.2 27.7 - - + +
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Residues in contact with GLY 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D VAL* 5.3 0.2 - - - -
130D ALA* 3.8 27.5 - - - +
134D LYS* 4.3 11.4 - - - +
185D LEU 3.4 5.3 + - - -
186D LEU 3.3 0.4 - - - -
187D HIS* 1.3 78.9 - - - +
189D ALA* 1.3 58.4 + - - +
191D GLU* 3.7 14.6 + - - +
192D HIS* 3.0 28.5 - - - -
210D GLN* 5.1 0.4 - - - -
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D VAL* 4.8 8.3 - - + -
185D LEU 3.3 9.4 + - - +
186D LEU 3.1 10.9 + - - +
187D HIS 3.1 0.4 - - - -
188D GLY* 1.3 73.6 - - - +
190D LEU* 1.3 56.7 + - - +
191D GLU 3.0 1.3 - - - -
192D HIS* 2.6 36.1 + - - +
193D TYR 3.1 3.5 + - - -
208D LEU* 3.4 21.8 - - + +
210D GLN* 5.0 1.3 - - - +
238D SER* 5.9 0.2 - - - +
240D VAL* 3.7 31.9 - - + -
242D PHE* 4.9 0.2 - - - -
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D LEU* 3.2 23.0 + - + +
187D HIS* 3.3 8.5 + - - +
189D ALA* 1.3 70.1 - - - +
191D GLU* 1.3 54.1 + - - +
192D HIS 2.6 16.5 + - - -
193D TYR* 2.9 20.6 + - - +
240D VAL* 4.1 9.2 - - + -
242D PHE* 3.4 31.9 - - + -
310D GLU* 3.8 37.2 - - + -
311D LEU* 4.2 7.6 - - + +
314D MET* 3.2 29.4 - - + +
315D TYR* 2.9 12.3 + - - -
335D VAL* 3.5 13.9 - - + -
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Residues in contact with GLU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D LYS* 4.1 17.6 - - - +
187D HIS* 3.0 44.8 + - - +
188D GLY* 3.9 9.2 - - - +
189D ALA 3.0 1.2 + - - -
190D LEU* 1.3 73.7 - - - +
192D HIS* 1.3 66.2 + - + +
195D ASN* 5.5 2.4 - - - +
314D MET* 3.2 17.9 - - + +
315D TYR* 3.4 14.4 + - + -
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Residues in contact with HIS 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B SER* 3.7 19.4 + - - -
97B PRO 4.9 8.1 + - - -
99B PHE 3.5 25.1 - - - -
100B GLY* 5.3 1.7 - - - -
101B PRO* 6.0 0.2 - - - +
128D VAL* 3.4 22.0 - - + +
129D ASP 3.9 15.5 + - - -
130D ALA* 5.1 1.1 - - - -
188D GLY 3.0 23.8 - - - -
189D ALA 2.6 17.4 + - - +
190D LEU 2.6 1.4 + - - -
191D GLU* 1.3 79.7 + - + +
193D TYR* 1.3 63.6 + - - +
194D VAL 3.4 1.8 - - - -
195D ASN* 3.3 9.6 + - - +
196D CYS* 2.8 38.5 + - - +
208D LEU* 3.5 15.5 - - + -
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Residues in contact with TYR 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D ALA 3.1 4.2 + - - -
190D LEU 2.9 13.4 + - - +
192D HIS* 1.3 81.7 - - - +
194D VAL* 1.3 81.2 + - + +
196D CYS 3.0 5.7 + - - -
197D LEU* 3.0 38.0 + - + +
204D LEU* 3.6 7.4 - - + +
206D TYR* 2.9 32.4 + + - -
208D LEU* 4.1 0.9 - - - +
242D PHE* 3.5 51.4 - + + -
311D LEU* 3.9 30.1 - - + -
322D LEU* 3.0 33.4 + - + -
333D PRO* 3.0 22.6 - - + +
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Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D LEU 4.4 1.0 + - - -
192D HIS 3.4 0.4 - - - -
193D TYR* 1.3 84.5 - - + +
195D ASN* 1.3 63.6 + - - +
197D LEU* 3.2 21.6 + - - +
198D ASP* 4.1 2.8 + - - +
315D TYR* 3.9 26.0 + - + +
321D LYS* 3.9 41.1 - - + +
322D LEU* 3.3 33.9 - - + -
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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