Contacts of the strand formed by residues 184 - 191 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C HIS* 3.6 5.4 - - - -
165C ARG 4.3 0.2 - - - -
166C PHE* 3.3 7.6 - - - +
167C SER* 2.7 45.2 + - - +
183C ARG* 1.3 74.8 - - - +
185C PHE* 1.3 59.8 - - - +
186C ALA 4.1 0.7 - - - -
201C ASN* 3.4 14.8 - - - -
269C MET* 4.0 4.9 - - - +
760C HDD 3.5 10.3 - - - -
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Residues in contact with PHE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C VAL* 3.9 5.2 - - + -
165C ARG 3.9 2.7 - - - -
166C PHE* 3.8 26.7 - + - -
184C GLY* 1.3 74.1 - - - +
186C ALA* 1.3 59.2 + - - +
187C THR* 3.6 21.7 + - - -
198C LEU 3.6 3.5 - - - +
200C GLY* 2.7 37.4 + - - +
201C ASN 4.6 7.2 - - - +
269C MET* 4.3 14.1 - - + -
270C GLU 4.4 1.6 - - - -
271C GLY* 3.6 20.6 - - - -
293C TRP* 3.6 41.5 + + + -
334C TYR* 3.8 36.8 - + - -
373C MET* 3.8 8.7 - - + -
760C HDD 3.7 0.4 - - - +
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Residues in contact with ALA 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C VAL* 3.1 6.3 - - - +
165C ARG 2.9 40.0 + - - +
185C PHE* 1.3 74.4 - - - +
187C THR* 1.3 61.7 + - - +
198C LEU 3.4 5.8 - - - +
199C VAL* 4.2 5.6 - - - +
391C PHE* 3.7 30.5 - - + -
760C HDD 4.0 26.9 - - + +
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Residues in contact with THR 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C VAL* 3.8 11.4 - - + -
163C PHE 3.6 2.5 - - - -
164C VAL* 3.7 6.6 - - + +
185C PHE* 3.6 23.6 - - - -
186C ALA* 1.3 76.8 + - - +
188C LYS* 1.3 61.4 + - - +
189C PHE* 3.5 29.2 - - + -
196C PHE 3.7 1.2 - - - +
197C ASP* 3.4 3.6 - - - +
198C LEU* 2.9 35.9 + - - -
293C TRP* 3.7 11.8 + - - -
373C MET* 3.6 25.4 - - - -
391C PHE* 4.1 3.1 - - - -
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Residues in contact with LYS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLN* 4.7 3.2 + - - -
162C VAL* 3.1 8.3 - - - -
163C PHE* 2.7 38.3 + - + +
187C THR* 1.3 72.8 - - - +
189C PHE* 1.3 60.7 + - - +
190C TYR* 3.3 41.4 - - + +
195C ILE* 3.7 19.8 - - + +
197C ASP* 2.8 36.5 + - - +
389C ALA* 5.4 2.2 - - - -
390C ALA 2.8 31.9 + - - +
391C PHE* 3.7 14.1 - - + -
395C HIS* 4.5 1.8 + - - -
433C ILE 4.1 3.6 - - - +
434C ASN* 3.9 20.0 + - - +
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Residues in contact with PHE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PHE* 3.8 29.8 - + + -
152C PHE* 4.1 18.8 - + - -
160C THR* 3.9 15.9 - - + -
161C PRO 3.8 3.1 - - - -
162C VAL* 3.7 15.0 - - + -
187C THR* 3.5 29.8 - - + -
188C LYS* 1.3 72.5 - - - +
190C TYR* 1.3 60.6 + - - +
191C THR* 3.1 16.0 + - + -
195C ILE* 3.4 4.9 - - - +
196C PHE* 2.7 75.7 + + + +
198C LEU* 4.0 12.3 - - + -
293C TRP* 3.7 19.3 - + - -
336C LEU* 4.8 4.0 - - + -
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Residues in contact with TYR 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLU* 5.0 1.6 - - - +
64C LYS* 3.4 43.4 - - + -
160C THR* 3.6 3.6 - - - +
161C PRO* 3.1 49.1 + - + +
162C VAL 4.0 1.8 - - - -
163C PHE* 3.5 28.3 - - + +
188C LYS* 3.3 35.5 - - + +
189C PHE* 1.3 69.2 - - - +
191C THR* 1.3 62.1 + - - +
192C GLU* 5.6 0.7 - - - +
195C ILE* 3.4 24.5 - - + -
433C ILE* 2.7 29.1 + - - +
435C ARG 3.6 13.2 - - - -
437C THR* 3.7 24.3 + - + +
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Residues in contact with THR 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ASP* 5.4 0.8 - - - +
152C PHE* 3.7 46.4 - - + -
160C THR* 4.2 5.4 - - + -
189C PHE* 3.1 21.7 + - + +
190C TYR* 1.3 77.0 - - - +
192C GLU* 1.3 62.2 + - - +
193C GLU* 3.1 16.7 + - - +
194C GLY 2.5 33.2 + - - +
195C ILE* 5.9 0.2 - - - +
196C PHE* 4.3 7.9 - - + -
397C VAL* 3.9 6.8 - - + +
437C THR* 4.3 4.6 + - - -
438C CYS* 3.6 11.8 - - - +
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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