Contacts of the strand formed by residues 163 - 170 (chain L) in PDB entry 4GUN
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 LEU 163 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I ASP* 5.6 1.8 - - - +
302I SO4 5.7 4.0 - - - +
61K LYS* 2.7 33.8 + - - -
138L VAL* 4.0 20.6 - - + -
139L LYS 3.5 2.5 - - - +
140L ASN* 3.8 38.6 - - + +
150L VAL* 6.1 3.6 - - + -
158L ILE* 3.5 28.3 - - + +
160L ALA* 3.1 21.0 + - + +
161L PRO 4.2 0.4 - - - +
162L HIS* 1.3 96.3 - - + +
164L VAL* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K LYS* 4.8 2.2 - - - +
138L VAL* 3.3 5.4 - - - -
139L LYS* 2.8 50.7 + - + +
141L LYS* 3.8 36.6 - - + +
158L ILE* 4.6 0.2 - - - -
163L LEU* 1.3 77.7 - - - +
165L PRO* 1.4 78.2 - - + +
166L ILE* 3.4 5.6 + - + +
203L ARG* 3.8 24.5 - - + +
206L ALA* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 165 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K LYS* 4.8 7.0 - - + +
78L THR* 6.3 0.2 - - + -
82L LEU* 3.8 37.9 - - + +
136L PHE* 4.1 18.4 - - + -
137L ILE 3.9 5.4 - - - +
138L VAL* 4.4 5.4 - - + -
158L ILE* 4.1 24.2 - - + +
163L LEU 4.1 5.6 - - - +
164L VAL* 1.4 93.8 - - + +
166L ILE* 1.3 59.4 + - - +
167L ILE 5.3 2.0 - - - +
203L ARG* 3.5 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L LEU* 4.0 18.2 - - + -
137L ILE* 2.7 25.9 + - + +
138L VAL 4.0 2.0 - - - -
139L LYS* 3.7 23.3 - - + +
147L LEU* 4.4 5.8 - - + -
164L VAL* 3.5 22.0 - - + +
165L PRO* 1.3 77.2 - - - +
167L ILE* 1.3 68.3 + - + +
197L TRP* 5.4 1.3 - - + -
200L ALA* 3.7 30.4 - - + +
203L ARG* 3.0 31.2 + - - +
204L TYR* 3.7 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L ASN* 3.5 22.4 - - + +
136L PHE* 3.2 10.3 - - - +
137L ILE* 3.0 46.3 + - + +
165L PRO* 5.2 0.9 - - - -
166L ILE* 1.3 83.8 - - + +
168L ALA* 1.4 61.6 + - - +
169L ILE* 3.8 31.0 - - + -
192L TRP* 4.4 4.0 - - + -
195L ILE* 3.7 26.5 - - + -
196L ASN 4.0 2.9 - - - +
197L TRP* 3.9 24.5 - - + -
200L ALA* 3.6 22.2 - - + -
203L ARG* 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L ASN 4.4 0.2 - - - +
82L LEU* 3.9 21.8 - - + -
83L PHE* 3.3 12.0 - - - +
86L ASN* 2.8 33.0 + - - +
134L TRP* 4.1 14.4 - - + -
135L ALA 3.7 4.5 - - - -
136L PHE* 3.7 25.8 - - + -
167L ILE* 1.4 72.4 - - - +
169L ILE* 1.4 63.5 + - - +
203L ARG* 4.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L PHE* 4.1 1.6 - - - -
122L THR* 4.7 4.9 - - + -
126L LEU* 3.8 36.9 - - + +
134L TRP* 3.3 10.1 - - - -
135L ALA 2.9 35.7 + - - +
167L ILE* 3.8 17.3 - - + -
168L ALA* 1.4 73.3 - - - +
170L ASP* 1.3 70.1 + - - +
171L ALA 3.5 0.5 + - - -
187L TYR* 4.7 0.9 - - - +
188L PHE* 4.7 4.3 - - + -
191L ILE* 4.0 31.0 - - + -
192L TRP* 4.1 16.4 - - + -
195L ILE* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L HIS* 2.8 8.7 + - - -
80L HIS* 3.4 1.9 + - - -
83L PHE* 3.5 25.4 - - + -
134L TRP* 3.5 25.7 - - + -
169L ILE* 1.3 73.4 - - - +
171L ALA* 1.3 60.0 + - - +
172L TRP* 3.1 35.5 + - - +
175L ALA* 3.8 11.3 - - + +
187L TYR* 2.9 31.5 + - - -
301L MN 2.0 35.4 + - - -
----------------------------------------------------------
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