Contacts of the strand formed by residues 170 - 178 (chain A) in PDB entry 3GG0
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 GLN 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A HIS* 3.6 20.7 + - - -
164A LEU* 3.7 11.4 + - - +
167A GLN* 3.9 8.3 - - - +
169A CYS* 1.3 75.4 - - - +
171A PHE* 1.3 69.2 + - - +
191A ILE* 3.6 2.4 - - - +
192A ARG* 2.6 33.3 + - + +
193A SER 3.1 16.7 + - - +
194A PRO* 2.9 28.6 + - - -
195A THR 4.4 0.2 - - - -
196A GLY* 3.5 13.7 - - - +
221A TYR* 5.7 0.7 - - - -
388A LEU* 3.9 17.2 - - + +
389A ASN* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A CYS* 3.7 16.2 - - - -
170A GLN* 1.3 83.8 - - - +
172A ALA* 1.3 56.6 + - - +
189A ALA* 3.7 22.2 - - + -
190A LEU 3.4 7.2 - - - -
191A ILE* 3.5 38.8 - - + -
218A SER* 3.2 39.0 - - - -
219A LYS* 4.3 7.6 - - + -
221A TYR* 4.3 4.5 - - + -
222A ALA* 3.9 26.2 - - + -
225A LEU* 3.6 18.3 - - + +
388A LEU* 3.7 4.7 - - - +
389A ASN* 2.8 39.2 + - - +
501A C2E 3.8 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 1.3 75.8 - - - +
173A LEU* 1.3 63.5 + - - +
188A GLU 3.5 0.3 - - - +
189A ALA* 3.4 4.5 - - - -
190A LEU* 2.8 34.4 + - + +
192A ARG* 3.9 35.5 - - + +
386A PRO* 4.0 4.7 - - + -
387A CYS 3.3 26.2 - - - +
388A LEU* 3.9 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA* 1.3 74.8 - - - +
174A GLN* 1.3 60.1 + - - +
175A ALA 4.3 0.3 + - - -
187A PHE* 4.0 28.8 - - + -
188A GLU 3.3 12.1 - - - +
189A ALA* 3.9 18.6 - - + +
222A ALA 6.0 1.1 - - - +
225A LEU* 3.8 31.9 - - + +
226A ALA* 5.8 2.0 - - + +
229A LEU* 4.0 26.9 - - + -
236A LEU* 4.2 10.8 - - + -
384A SER* 5.1 0.3 + - - -
385A ARG 3.8 2.8 - - - +
386A PRO* 3.5 2.4 - - - +
387A CYS* 3.0 31.1 + - - +
390A GLY 3.7 24.4 - - - +
391A ILE* 5.1 1.3 - - + -
392A GLY 4.9 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 1.3 75.0 - - - +
175A ALA* 1.3 71.6 + - - +
176A ILE* 3.6 1.0 + - - +
187A PHE* 3.3 4.2 - - - -
188A GLU* 2.7 39.6 + - - +
190A LEU* 4.2 10.8 - - + +
379A GLN* 2.9 29.0 + - - +
380A GLY* 3.6 14.8 - - - +
381A PHE* 4.1 0.4 - - - -
384A SER* 2.9 30.2 + - - +
386A PRO* 4.0 19.0 - - + +
501A C2E 3.1 43.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU 4.3 0.4 + - - -
174A GLN* 1.3 83.7 - - - +
176A ILE* 1.3 60.4 + - - +
177A VAL* 4.0 16.7 + - + +
184A VAL* 4.2 9.4 - - + -
186A SER 3.5 4.9 - - - -
187A PHE* 3.8 23.5 - - + -
378A PHE 4.3 2.3 - - - +
379A GLN* 4.1 9.0 - - - +
380A GLY 4.9 0.9 + - - -
383A PHE* 5.8 0.9 - - - +
384A SER* 3.6 27.9 + - - +
394A ILE* 4.4 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLN 4.1 0.4 - - - +
175A ALA* 1.3 72.7 - - - +
177A VAL* 1.3 62.3 + - - +
184A VAL* 3.7 2.9 - - - +
185A SER* 2.8 34.9 + - - -
186A SER* 2.7 40.4 + - - +
187A PHE 4.3 0.4 - - - -
188A GLU* 4.0 24.0 - - + +
237A ALA* 5.0 4.0 - - + -
321A LYS* 4.9 2.9 - - + +
323A LYS* 4.7 6.1 - - - +
357A VAL* 4.0 29.4 - - + -
377A LEU* 4.3 9.6 - - + -
378A PHE 3.5 9.0 - - - +
379A GLN* 3.4 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA* 4.0 21.3 - - + +
176A ILE* 1.3 77.5 - - - +
178A GLU* 1.3 60.5 + - - +
179A PRO* 3.4 13.3 - - + +
183A ARG 3.6 3.8 - - - +
184A VAL* 4.8 4.0 - - + -
185A SER* 4.8 0.7 - - - -
377A LEU* 3.5 7.2 - - - +
378A PHE* 2.8 43.3 + - + +
383A PHE* 3.6 37.9 - - + -
384A SER* 5.1 0.7 - - - -
394A ILE* 4.3 12.8 - - + -
396A TRP* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 1.3 73.4 - - - +
179A PRO* 1.3 58.7 - - - +
180A ALA* 4.4 7.7 - - + +
181A LYS* 2.9 52.3 + - - +
182A LYS 3.1 8.1 + - - -
183A ARG* 2.7 56.7 + - - +
185A SER* 4.7 0.6 - - - +
376A ARG* 3.7 27.7 - - + +
377A LEU* 3.7 16.5 - - + +
396A TRP* 4.2 0.4 - - - -
121B VAL* 5.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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