Contacts of the strand formed by residues 194 - 201 (chain D) in PDB entry 1GGE
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 GLY 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B GLN 3.3 13.0 - - - -
85B GLY 3.7 5.4 - - - -
86B VAL* 4.1 2.0 - - - -
191D THR* 2.6 40.3 + - - +
193D GLU* 1.3 80.0 - - - +
195D ILE* 1.3 67.4 + - - -
397D VAL* 3.5 5.1 - - - +
438D CYS* 3.4 13.8 - - - -
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Residues in contact with ILE 195 (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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84B GLN* 2.9 44.3 + - + +
86B VAL* 4.7 2.3 - - - +
188D LYS* 3.7 15.3 - - + +
189D PHE 3.4 6.1 - - - +
190D TYR* 3.4 40.4 - - + -
194D GLY* 1.3 73.0 - - - -
196D PHE* 1.3 61.9 + - - +
197D ASP* 3.4 29.8 - - - +
395D HIS* 3.4 17.8 - - - +
396D ILE 4.0 2.3 - - - +
397D VAL* 3.7 7.4 - - - +
434D ASN 4.3 5.6 - - - +
435D ARG 4.3 0.2 - - - +
436D PRO* 3.8 22.9 - - + -
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Residues in contact with PHE 196 (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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152D PHE* 3.6 27.8 - + - -
189D PHE* 2.7 78.2 + + + +
191D THR* 4.5 4.3 - - + -
194D GLY 3.5 1.0 + - - -
195D ILE* 1.3 73.5 - - - +
197D ASP* 1.3 73.3 + - - +
198D LEU* 3.8 22.9 - - + -
277D PHE* 6.1 3.1 - + - -
291D PHE* 4.4 21.8 - + - -
336D LEU* 6.3 1.1 - - + -
393D PRO 5.5 0.4 - - - -
395D HIS 3.2 10.8 - - - -
396D ILE* 4.1 10.8 - - + -
397D VAL* 4.2 17.5 - - + -
400D LEU* 3.5 27.4 - - + -
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Residues in contact with ASP 197 (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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187D THR 3.3 4.5 - - - +
188D LYS* 2.8 47.4 + - - +
195D ILE* 3.4 3.5 - - - +
196D PHE* 1.3 84.7 - - - +
198D LEU* 1.3 58.8 + - - +
199D VAL* 3.6 10.7 + - + -
391D PHE* 3.2 7.2 - - + -
392D HIS 2.9 31.3 + - - +
393D PRO* 3.8 15.2 - - - +
395D HIS* 2.8 36.9 + - - +
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Residues in contact with LEU 198 (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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185D PHE 3.7 2.1 - - - +
186D ALA* 3.5 2.3 - - - -
187D THR* 2.8 34.4 + - - +
189D PHE* 4.0 10.3 - - + -
196D PHE* 3.8 25.4 + - + -
197D ASP* 1.3 70.0 - - - +
199D VAL* 1.3 63.5 + - - +
200D GLY* 3.6 3.7 + - - +
272D PHE 6.1 0.7 - - - -
273D GLY* 4.2 15.3 - - - +
277D PHE* 5.3 5.4 - - + -
291D PHE* 3.4 51.4 - - + -
293D TRP* 4.2 22.2 + - + +
336D LEU* 4.1 20.4 - - + -
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Residues in contact with VAL 199 (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 ALA* 4.2 7.9 - - + +
197D ASP* 3.6 20.0 + - + +
198D LEU* 1.3 78.5 - - - +
200D GLY* 1.3 57.9 + - - +
273D GLY 4.6 2.9 - - - +
391D PHE* 3.9 8.3 - - + -
392D HIS 3.8 9.0 - - - +
393D PRO* 3.7 27.8 - - + +
411D ARG* 3.1 39.0 + - - +
415D TYR* 4.2 7.0 - - + -
760D HDD 3.5 43.0 - - + +
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Residues in contact with GLY 200 (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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185D PHE* 2.8 42.8 + - - -
198D LEU* 3.6 3.3 + - - +
199D VAL* 1.3 76.2 - - - +
201D ASN* 1.3 66.7 + - - +
272D PHE 3.1 18.6 - - - -
273D GLY* 4.3 3.8 - - - -
293D TRP* 6.6 0.4 - - - -
760D HDD 3.2 10.8 - - - +
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Residues in contact with ASN 201 (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 HIS* 3.4 13.3 + - - -
169D VAL* 5.2 0.8 - - - +
182D ILE* 3.6 22.1 - - + +
183D ARG 3.1 11.0 - - - +
184D GLY* 3.4 12.5 - - - -
185D PHE* 4.5 4.3 - - - -
200D GLY* 1.3 82.1 - - - +
202D ASN* 1.3 60.2 + - - +
203D THR* 3.3 5.7 + - - +
205D ILE 5.4 0.6 + - - -
206D PHE* 3.8 22.8 - - - -
271D GLY* 3.4 3.5 - - - -
272D PHE* 2.7 34.1 + - - +
274D ILE* 4.1 14.1 - - + +
760D HDD 3.5 27.1 - - - +
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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