Contacts of the strand formed by residues 173 - 179 (chain L) in PDB entry 3GBN
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 TYR 173 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L ASP 3.1 24.8 + - - -
139L PHE* 3.1 47.6 + - + +
140L TYR* 5.1 4.0 - - + -
164L PRO* 4.7 8.5 - - + -
165L SER 3.4 8.3 - - - +
166L LYS* 4.5 1.6 - - + +
167L GLN* 3.7 2.8 + - - -
172L LYS* 1.3 76.6 - - - +
174L ALA* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H PHE* 4.8 9.2 - - + -
175H PRO* 5.1 5.4 - - + -
136L ILE 3.7 9.0 - - - +
137L SER* 4.7 1.1 - - - +
139L PHE* 4.0 2.8 - - - -
164L PRO* 3.1 4.7 - - - +
165L SER* 2.8 41.4 + - - +
167L GLN* 3.2 32.3 - - + +
172L LYS 4.3 0.2 + - - -
173L TYR* 1.3 71.4 - - - +
175L ALA* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H PHE* 3.0 25.0 - - - -
175H PRO* 5.7 1.3 - - - +
136L ILE* 3.1 29.5 + - + +
139L PHE* 4.1 14.4 - - + -
162L THR* 3.7 25.1 - - - +
163L THR 4.1 4.0 - - - +
164L PRO* 4.4 3.6 - - + -
174L ALA* 1.3 77.9 - - - +
176L SER* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174H PHE* 4.3 14.7 - - - +
175H PRO 4.4 2.3 + - - -
188H SER* 5.9 0.4 - - - -
133L VAL* 6.4 0.2 - - - -
134L CYS 3.4 14.8 - - - -
135L LEU* 4.4 7.6 - - - -
136L ILE* 4.6 5.4 - - - -
161L THR* 3.4 2.8 - - - -
162L THR* 2.6 54.2 + - - +
175L ALA* 1.3 81.3 - - - +
177L SER* 1.3 58.5 + - - +
178L TYR* 3.8 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L CYS* 2.9 43.3 + - - +
136L ILE* 5.1 6.5 - - - +
159L VAL* 4.4 8.8 - - - +
160L GLU 3.5 6.1 + - - -
161L THR* 2.9 28.8 - - - -
176L SER* 1.3 71.3 + - - +
178L TYR* 1.3 68.2 + - - +
194L CYS* 5.1 6.5 - - - -
195L GLN* 5.7 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H LEU* 3.7 29.6 - - + -
145H LYS* 5.2 9.2 - - - +
177H VAL* 3.7 30.5 + - + -
186H SER* 4.8 4.0 - - - -
187H LEU* 3.2 6.2 - - - -
188H SER* 2.8 36.6 + - - -
131L THR* 5.1 6.5 - - - -
132L LEU 3.1 14.8 - - - +
133L VAL* 4.2 17.5 - - + -
158L GLY 3.8 1.0 - - - +
159L VAL* 3.8 3.9 - - - +
160L GLU* 3.0 43.3 + - + +
176L SER* 3.8 27.4 + - - -
177L SER* 1.3 81.1 - - - +
179L LEU* 1.3 61.7 + - - +
180L SER* 4.0 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L ALA 4.0 0.7 - - - +
131L THR* 3.3 4.6 - - - -
132L LEU* 2.8 50.1 + - + +
158L GLY 3.6 32.3 - - - +
159L VAL* 4.1 15.0 - - + +
178L TYR* 1.3 72.4 - - - +
180L SER* 1.3 64.9 + - - +
----------------------------------------------------------
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