Contacts of the helix formed by residues 210 - 218 (chain D) in PDB entry 1GUL
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 GLU 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209D ASP* 1.3 75.1 - - + +
211D ILE* 1.3 74.0 + - + +
213D VAL* 3.7 7.5 - - + +
214D ARG* 2.9 45.5 + - - +
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Residues in contact with ILE 211 (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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209D ASP* 2.9 16.8 - - + +
210D GLU* 1.3 95.4 - - + +
212D TYR* 1.3 59.6 + - - +
214D ARG* 2.9 9.0 + - + +
215D THR* 2.7 45.0 + - - +
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Residues in contact with TYR 212 (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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9D TYR* 4.2 5.3 - + - -
10D PRO* 4.2 11.7 - - + +
11D ASN 3.9 9.6 - - - +
12D GLY* 3.6 32.3 - - - -
13D ARG 5.1 0.9 - - - -
14D GLY* 3.4 31.5 + - - -
110D PRO* 5.4 0.7 - - + -
111D PHE* 3.9 16.8 - + - -
208D PRO* 3.5 30.5 - - + -
209D ASP* 2.7 26.9 + - - +
211D ILE* 1.3 74.5 - - - +
213D VAL* 1.3 64.7 + - + +
215D THR* 3.0 7.1 + - + -
216D VAL* 2.7 59.4 + - + +
301D IBG 3.8 13.9 - - - +
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Residues in contact with VAL 213 (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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110D PRO* 3.8 36.1 - - + +
111D PHE* 3.8 15.7 - - + -
208D PRO* 4.7 2.7 - - + +
209D ASP 2.9 19.8 + - - +
210D GLU* 3.7 7.6 - - - +
212D TYR* 1.3 90.6 - - + +
214D ARG* 1.3 63.0 + - - +
216D VAL* 3.1 2.4 + - - +
217D TYR* 3.1 44.1 + - + -
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Residues in contact with ARG 214 (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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210D GLU* 2.9 29.9 + - - +
211D ILE* 2.9 13.0 + - + +
213D VAL* 1.3 77.4 - - - +
215D THR* 1.3 64.7 + - - +
217D TYR* 3.1 15.7 + - - +
218D ASN* 2.8 46.8 + - - +
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Residues in contact with THR 215 (chain D).
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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10D PRO* 5.2 3.8 - - + -
11D ASN 6.2 0.2 - - - +
35D LEU 4.6 3.1 - - - +
36D GLU* 4.0 16.4 - - + +
211D ILE* 2.7 28.7 + - - +
212D TYR* 3.3 12.1 - - + -
214D ARG* 1.3 76.8 - - - +
216D VAL* 1.3 68.4 + - + +
218D ASN* 2.9 17.3 + - - +
219D ILE* 2.9 35.0 + - + +
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Residues in contact with VAL 216 (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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10D PRO* 4.5 12.3 - - + -
111D PHE* 3.0 41.1 - - + -
212D TYR* 2.7 59.9 + - + +
213D VAL 3.5 2.5 - - - +
215D THR* 1.3 73.4 - - - +
217D TYR* 1.3 68.8 + - + +
219D ILE* 2.9 13.8 + - - -
220D PHE* 3.0 35.7 + - + +
301D IBG 5.4 5.8 - - + -
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Residues in contact with TYR 217 (chain D).
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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38D LYS* 4.3 1.6 + - - -
110D PRO 5.1 0.2 + - - -
111D PHE* 3.7 41.7 + + + +
213D VAL* 3.1 42.6 + - + -
214D ARG* 3.3 15.9 - - - +
216D VAL* 1.3 80.3 - - + +
218D ASN* 1.3 71.0 + - - +
219D ILE 3.2 0.5 + - - -
220D PHE* 3.3 21.1 - - - +
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Residues in contact with ASN 218 (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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36D GLU 5.4 3.4 - - - +
37D THR* 6.0 1.1 - - - -
38D LYS* 3.1 26.7 + - - +
214D ARG* 2.8 46.2 + - - +
215D THR* 2.9 10.2 + - - +
217D TYR* 1.3 88.9 + - - +
219D ILE* 1.3 59.5 + - + +
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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