Contacts of the helix formed by residues 213 - 222 (chain B) in PDB entry 1GV3
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 ARG 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LEU* 5.9 1.4 - - - +
209B ARG 3.5 19.2 + - - -
210B TYR* 3.0 39.6 + - + +
211B GLN* 3.2 25.4 + - - +
212B ASN* 1.3 91.2 + - - +
214B ARG* 1.3 64.2 + - - +
215B PRO* 3.3 9.6 - - + -
216B GLU* 3.1 55.3 + - + +
217B TYR 3.5 3.3 + - - -
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Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TRP* 5.6 4.2 - - - -
158B GLY 2.9 26.5 + - - -
159B GLY* 3.8 13.4 + - - -
161B ARG 2.7 25.0 + - - -
163B GLY 3.1 26.9 + - - +
201B VAL* 3.4 29.3 + - + +
203B GLU* 5.3 3.4 - - - +
206B TYR* 3.1 48.3 + - + +
212B ASN 3.0 10.0 + - - +
213B ARG* 1.3 70.5 - - - +
215B PRO* 1.3 72.8 - - + +
217B TYR* 3.0 6.7 + - + +
218B LEU* 2.9 36.1 + - + +
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Residues in contact with PRO 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLY* 6.1 3.1 - - - -
212B ASN 4.7 1.6 - - - +
213B ARG* 3.4 7.2 - - + -
214B ARG* 1.3 94.7 - - + +
216B GLU* 1.3 62.6 + - + +
218B LEU* 3.4 13.9 + - + +
219B ASN* 3.0 34.4 + - - +
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B TYR* 3.8 16.2 - - + -
213B ARG* 3.1 56.2 + - + +
215B PRO* 1.3 76.9 - - + +
217B TYR* 1.3 65.6 + - - +
219B ASN* 3.3 9.5 + - - +
220B ASN* 3.0 29.1 + - - +
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Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ALA* 4.7 2.2 - - + -
54B ILE* 4.2 21.9 - - + +
120B PHE* 3.6 17.2 - - - -
199B ASN* 2.8 34.7 + - - -
200B ASP 3.4 22.3 + - - -
201B VAL* 5.7 0.4 - - + -
205B ALA* 3.9 18.5 + - + +
206B TYR* 3.5 37.7 - + + -
210B TYR* 3.7 34.7 - + + -
213B ARG 3.5 2.2 + - - +
214B ARG* 3.0 11.1 + - + +
216B GLU* 1.3 76.6 - - - +
218B LEU* 1.3 71.9 + - + +
220B ASN* 3.3 1.4 + - - +
221B TRP* 2.9 34.6 + + + +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B PHE* 5.4 4.7 - - + -
155B ASN* 3.6 43.2 - - + +
158B GLY* 3.8 8.5 - - - -
159B GLY* 3.7 16.8 - - - +
167B VAL* 5.6 0.2 - - + -
199B ASN* 3.5 27.2 + - + +
201B VAL* 4.0 19.7 - - + -
214B ARG* 2.9 30.5 + - + +
215B PRO* 3.7 14.6 - - + +
217B TYR* 1.3 83.2 - - + +
219B ASN* 1.3 60.6 + - - +
221B TRP* 3.7 7.3 + - - +
222B TRP* 3.1 22.2 + - - -
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Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LYS* 4.9 8.5 + - - -
155B ASN* 3.5 17.0 + - - +
215B PRO* 3.0 27.4 + - - +
216B GLU* 3.6 10.6 - - - +
217B TYR 3.2 0.2 - - - -
218B LEU* 1.3 77.5 - - - +
220B ASN* 1.3 65.6 + - - +
222B TRP* 3.3 23.5 + - - +
223B ASN* 4.6 3.5 + - - -
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Residues in contact with ASN 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS 4.2 8.9 + - - +
53B ALA* 3.4 19.9 - - - +
209B ARG* 4.8 5.1 - - - +
210B TYR* 3.1 39.1 + - - +
216B GLU* 3.0 15.0 + - - +
217B TYR 4.0 1.3 - - - +
219B ASN* 1.3 75.9 - - - +
221B TRP* 1.3 64.2 + - - +
222B TRP 3.1 2.9 - - - -
223B ASN* 3.0 30.4 + - - +
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Residues in contact with TRP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ALA* 4.2 6.7 - - - +
54B ILE* 4.5 3.6 - - + -
120B PHE* 3.7 8.7 - + - -
123B ILE* 4.0 16.6 - - + -
124B MET* 3.3 34.5 - - + +
154B PHE* 3.9 18.6 - + - -
197B MET* 3.7 32.3 - - + -
198B GLY 3.5 26.5 - - - -
199B ASN* 3.4 26.5 - - + +
217B TYR* 2.9 40.3 + + + +
218B LEU 3.7 4.5 - - - +
219B ASN 3.3 0.6 - - - -
220B ASN* 1.3 77.4 - - - +
222B TRP* 1.3 72.6 - + - +
223B ASN 3.1 1.6 + - - -
224B VAL* 3.1 22.6 + - + +
225B VAL* 3.6 26.9 - - + +
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Residues in contact with TRP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLY* 3.3 15.4 - - - -
130B GLY 4.6 3.3 + - - +
147B PHE* 4.4 12.8 - + + -
150B PHE* 3.6 30.1 - + - -
151B LYS* 3.6 37.9 - - + +
154B PHE* 3.3 39.5 - + + -
155B ASN* 2.9 26.8 + - - +
197B MET* 3.8 25.4 - - + -
218B LEU 3.1 21.2 + - - -
219B ASN 3.3 15.7 - - - +
220B ASN 3.1 0.8 - - - -
221B TRP* 1.3 82.2 - + - +
223B ASN* 1.3 62.3 + - - +
224B VAL 3.2 1.9 + - - -
225B VAL* 3.6 21.6 + - + +
227B TRP* 4.2 17.2 + + - -
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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