Contacts of the strand formed by residues 184 - 191 (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 184 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D HIS* 3.5 5.9 - - - -
165D ARG 4.3 0.2 - - - -
166D PHE* 3.2 8.6 - - - +
167D SER* 2.7 44.5 + - - +
183D ARG* 1.3 74.7 - - - +
185D PHE* 1.3 60.7 + - - +
186D ALA 4.1 0.9 - - - -
200D GLY 3.5 1.3 - - - -
201D ASN* 3.4 15.3 - - - -
269D MET* 4.0 4.2 - - - +
760D HDD 3.5 7.2 - - - -
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Residues in contact with PHE 185 (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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164D VAL* 3.9 4.5 - - + -
165D ARG 3.8 3.8 - - - -
166D PHE* 3.8 28.7 - + + -
184D GLY* 1.3 73.7 - - - +
186D ALA* 1.3 59.6 + - - +
187D THR* 3.6 14.8 - - - -
198D LEU* 3.7 3.6 - - - +
200D GLY* 2.8 36.2 + - - +
201D ASN 4.5 7.2 - - - +
269D MET* 4.2 13.9 - - + -
270D GLU 4.4 1.3 - - - -
271D GLY* 3.6 20.4 - - - -
293D TRP* 3.5 48.3 + + + -
334D TYR* 3.8 33.4 - + - -
373D MET* 3.8 12.3 - - + -
760D HDD 3.8 0.6 - - - +
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Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D VAL* 3.1 6.8 - - - +
165D ARG 2.8 41.6 + - - +
185D PHE* 1.3 74.2 - - - +
187D THR* 1.3 61.0 + - - +
198D LEU 3.5 4.9 - - - +
199D VAL* 4.2 9.2 - - + +
391D PHE* 3.7 29.1 - - + -
760D HDD 3.9 25.6 - - + +
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Residues in contact with THR 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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162D VAL* 3.8 11.9 - - + -
163D PHE 3.7 2.5 - - - -
164D VAL* 3.6 8.9 - - + +
185D PHE* 3.6 22.2 - - - -
186D ALA* 1.3 76.6 - - - +
188D LYS* 1.3 62.9 + - - +
189D PHE* 3.5 30.0 + - + -
196D PHE 3.7 0.9 - - - +
197D ASP* 3.3 3.1 - - - +
198D LEU* 2.8 40.4 + - - -
293D TRP* 3.7 11.6 + - - -
373D MET* 3.7 22.7 - - - -
391D PHE* 4.0 3.6 - - - -
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Residues in contact with LYS 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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84B GLN* 4.8 3.8 + - - -
162D VAL* 3.1 26.0 - - - +
163D PHE* 2.9 21.6 + - + +
187D THR* 1.3 72.7 - - - +
189D PHE* 1.3 60.1 + - - +
190D TYR* 3.4 38.8 - - + +
195D ILE* 3.7 20.7 - - + +
197D ASP* 2.8 35.5 + - - +
389D ALA* 5.5 1.8 - - - -
390D ALA 2.9 31.4 + - - +
391D PHE* 3.6 14.3 - - + -
395D HIS* 4.4 2.2 + - - -
433D ILE* 4.1 4.3 - - - +
434D ASN* 3.9 19.1 + - - +
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Residues in contact with PHE 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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138D PHE* 3.7 32.3 - + + -
152D PHE* 4.0 17.7 - + - -
160D THR* 3.9 15.0 - - + -
161D PRO 3.8 3.1 - - - -
162D VAL* 3.7 15.0 - - + -
187D THR* 3.5 28.7 - - + -
188D LYS* 1.3 71.7 - - - +
190D TYR* 1.3 61.0 + - - +
191D THR* 3.2 15.4 + - + -
195D ILE* 3.4 5.6 - - - +
196D PHE* 2.7 68.5 + + + +
198D LEU* 4.0 10.1 - - + -
293D TRP* 3.8 20.0 - + - -
336D LEU* 4.8 6.3 - - + -
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Residues in contact with TYR 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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63D GLU* 4.9 1.6 - - - +
64D LYS* 3.4 36.6 - - + -
160D THR* 3.6 3.6 - - - +
161D PRO* 3.1 49.3 + - + +
162D VAL 3.9 2.2 - - - -
163D PHE* 3.6 27.0 - - + +
188D LYS* 3.4 34.9 - - + +
189D PHE* 1.3 70.4 - - - +
191D THR* 1.3 62.1 + - - +
192D GLU* 5.7 0.3 - - - +
195D ILE* 3.4 23.6 - - + -
433D ILE* 2.6 34.9 + - - +
435D ARG 3.6 13.2 - - - -
437D THR* 3.7 24.1 + - + +
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Residues in contact with THR 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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151D ASP* 5.4 1.0 - - - +
152D PHE* 3.7 44.8 + - + -
160D THR* 4.1 4.7 - - + -
189D PHE* 3.2 20.8 + - + +
190D TYR* 1.3 77.0 - - - +
192D GLU* 1.3 64.2 + - - +
193D GLU* 3.1 16.6 + - - +
194D GLY 2.6 33.5 + - - +
196D PHE* 4.5 6.5 - - + -
397D VAL* 4.0 6.5 - - + +
437D THR* 4.4 4.5 + - - -
438D CYS* 3.5 13.2 - - - +
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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
------------------------------------------------------------
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