Contacts of the helix formed by residues 198 - 207 (chain B) in PDB entry 1GGT
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 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B HIS* 4.5 8.1 + - - -
187B TRP* 2.9 28.8 + - - -
196B ASP 4.3 0.4 + - - -
197B ASN* 1.3 71.9 + - - +
199B LYS* 1.3 59.8 + - + +
201B ARG* 2.5 60.4 + - - +
202B GLU* 2.9 36.9 + - - +
206B LEU* 5.4 1.2 - - - +
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Residues in contact with LYS 199 (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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197B ASN* 2.6 19.7 + - - +
198B GLU* 1.3 73.4 - - + +
200B GLU* 1.3 60.8 + - + +
202B GLU* 3.2 10.5 + - - +
203B GLU* 3.1 24.4 + - - +
469B ILE* 4.1 25.0 - - + +
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Residues in contact with GLU 200 (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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195B LEU* 3.4 26.1 - - + +
197B ASN* 2.8 35.4 + - + +
199B LYS* 1.3 77.4 - - - +
201B ARG* 1.3 53.3 + - - +
203B GLU* 4.7 0.4 - - - -
204B TYR* 2.7 69.4 + - + +
379B TRP* 5.4 2.3 - - - -
392B TRP* 4.7 6.8 + - - -
469B ILE* 3.6 19.7 - - + +
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Residues in contact with ARG 201 (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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186B PRO* 3.5 15.9 + - + -
187B TRP* 3.3 47.6 + - + +
194B TYR* 3.2 24.0 + - - -
195B LEU* 2.5 47.0 + - + -
196B ASP* 3.6 11.5 + - - +
197B ASN* 3.0 15.1 + - - +
198B GLU* 2.5 54.0 + - - +
200B GLU* 1.3 69.8 - - - +
202B GLU* 1.3 64.6 + - - +
205B VAL* 3.0 29.0 + - + +
206B LEU* 3.1 5.1 + - - +
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Residues in contact with GLU 202 (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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68B LYS* 5.9 0.7 + - - -
198B GLU* 2.9 39.3 + - + +
199B LYS* 3.2 9.1 + - - +
201B ARG* 1.3 75.4 - - - +
203B GLU* 1.3 56.0 + - - +
206B LEU* 2.9 25.7 + - + -
207B ASN* 2.7 34.0 + - - +
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Residues in contact with GLU 203 (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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199B LYS 3.1 13.1 + - - +
200B GLU 3.9 1.6 - - - +
202B GLU* 1.3 85.4 - - - +
204B TYR* 1.3 80.2 + - + +
205B VAL 3.2 0.5 + - - -
207B ASN* 3.4 22.5 + - - +
209B ILE 5.2 0.9 - - - +
210B GLY* 5.9 0.5 - - - -
227B TYR* 5.9 0.3 - - - -
326B ARG* 3.1 41.4 + - - -
467B LYS* 2.9 43.1 + - - +
468B GLN 4.3 3.4 - - - -
469B ILE* 3.9 33.1 - - + +
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Residues in contact with TYR 204 (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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195B LEU* 4.2 4.9 - - + -
200B GLU* 2.7 63.6 + - + +
203B GLU* 1.3 89.1 - - + +
205B VAL* 1.3 57.9 + - - +
326B ARG* 3.1 25.9 + - - +
331B PRO* 3.6 18.5 - - + +
332B ALA 3.2 15.3 + - - +
333B ARG* 3.6 47.2 + - + -
392B TRP* 3.8 22.2 - + - -
466B THR* 5.7 0.7 - - + +
467B LYS 5.2 7.8 + - - -
469B ILE* 3.7 20.1 - - + +
475B MET* 4.8 8.8 - - - +
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Residues in contact with VAL 205 (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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77B ARG* 4.6 5.2 - - - +
186B PRO* 4.0 20.9 - - + -
187B TRP* 4.5 16.4 - - + -
201B ARG* 3.0 23.6 + - + +
203B GLU 3.2 0.4 + - - -
204B TYR* 1.3 83.9 - - - +
206B LEU* 1.3 67.4 + - + +
207B ASN 3.4 1.1 - - - -
229B GLN* 2.8 24.8 + - - -
230B PHE* 4.4 2.6 - - - -
326B ARG* 3.8 23.9 - - - +
329B GLY* 4.4 11.4 - - - -
331B PRO* 3.7 28.0 - - + -
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Residues in contact with LEU 206 (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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65B HIS* 3.9 28.7 - - + +
68B LYS* 3.7 31.0 + - + +
77B ARG* 4.2 5.8 - - - +
187B TRP* 3.6 36.3 - - + -
198B GLU* 5.4 1.8 - - - +
201B ARG 3.1 0.8 + - - +
202B GLU* 2.9 33.0 + - + +
205B VAL* 1.3 83.0 - - + +
207B ASN* 1.3 57.7 + - - -
208B ASP* 3.4 3.3 + - - +
229B GLN* 3.8 0.9 - - - -
230B PHE* 3.1 40.5 - - + -
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Residues in contact with ASN 207 (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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202B GLU 2.7 12.1 + - - +
203B GLU* 3.4 38.5 + - - +
205B VAL 3.4 1.6 - - - -
206B LEU* 1.3 72.4 - - - +
208B ASP* 1.3 63.6 + - - +
209B ILE* 2.8 44.6 + - - +
227B TYR* 3.8 0.3 - - - -
229B GLN* 2.9 11.3 + - - +
326B ARG* 2.6 27.9 + - - +
467B LYS* 4.2 8.1 - - - +
703B ARG* 5.0 1.0 + - - -
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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