Contacts of the strand formed by residues 153 - 160 (chain C) in PDB entry 1GN2
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 ILE 153 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 6.4 0.2 - - + -
151A LEU* 4.0 23.1 - - + -
152A GLY* 3.1 26.1 + - - +
129C GLY* 4.4 5.2 - - - -
130C TRP 3.3 18.6 - - - +
131C ASP* 3.4 26.5 - - + +
140C PHE* 3.6 33.0 - - + -
150C PRO* 3.8 40.8 + - + +
151C LEU 3.3 2.4 - - - +
152C GLY* 1.3 77.5 - - - +
154C VAL* 1.3 71.5 + - - +
155C PRO* 3.4 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLY* 4.8 1.3 - - - -
129C GLY* 3.0 6.0 - - - -
130C TRP* 2.6 58.8 + - + +
132C THR* 4.1 12.6 - - + -
152C GLY 4.4 3.1 - - - +
153C ILE* 1.3 73.3 - - - +
155C PRO* 1.3 77.7 - - + +
156C LEU* 3.9 4.6 - - + +
193C ARG* 5.3 1.8 - - + +
197C ALA* 4.2 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 4.2 33.9 - - + +
152A GLY* 3.8 13.7 - - - +
74C VAL* 5.4 1.3 - - + -
78C ILE* 3.7 27.1 - - + +
127C ALA* 6.1 0.7 - - + -
128C LEU 3.9 5.4 - - - +
129C GLY* 4.3 1.3 - - - -
153C ILE* 3.4 11.5 - - + +
154C VAL* 1.3 94.5 - - + +
156C LEU* 1.3 67.1 + - - +
158C LEU* 4.6 9.0 - - + -
193C ARG* 4.0 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 4.6 2.6 - - - +
82C ASN* 3.4 10.4 + - - -
95C LEU* 5.5 1.3 - - + -
128C LEU* 2.9 33.1 + - + +
129C GLY 4.3 4.5 - - - -
130C TRP* 4.3 3.1 - - + -
137C LEU* 3.6 31.2 - - + -
154C VAL* 3.9 12.3 - - + +
155C PRO* 1.3 83.4 - - - +
157C LEU* 1.3 59.9 + - - +
190C VAL* 4.1 15.5 - - + +
193C ARG* 3.3 56.3 - - + +
194C TYR* 3.8 20.2 - - + +
197C ALA* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ASN* 3.3 26.7 - - + +
109C PHE* 4.4 10.5 - - + -
113C PHE* 4.2 16.3 - - + -
127C ALA* 3.2 1.2 - - - -
128C LEU* 2.8 41.0 + - + -
156C LEU* 1.3 80.1 - - - +
158C LEU* 1.3 69.4 + - - +
181C PHE* 3.9 23.6 - - + -
182C TRP* 4.4 14.6 - - + -
185C VAL* 4.1 9.2 - - + -
187C TRP* 4.2 27.1 - - + -
190C VAL* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 4.1 12.8 - - + -
75C ASN* 3.9 42.0 - - + +
78C ILE* 4.3 21.3 - - + -
79C TRP* 3.5 17.5 - - + -
82C ASN* 2.9 13.7 + - - +
113C PHE* 4.5 3.1 - - - -
125C TRP* 3.6 24.7 - - + -
126C ALA 3.3 3.6 - - - +
127C ALA* 3.0 33.4 - - + -
128C LEU 4.5 0.4 - - - +
155C PRO* 4.6 9.0 - - + -
157C LEU* 1.3 85.1 - - - +
159C LEU* 1.3 62.0 + - - +
160C ASP 4.1 0.4 - - - -
181C PHE* 3.8 10.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TRP* 3.8 3.1 - - + -
113C PHE* 3.8 25.6 - - + -
114C HIS* 6.1 1.6 - - - -
117C ALA* 4.1 15.7 - - + -
125C TRP* 3.3 4.0 - - - -
126C ALA* 2.9 28.9 + - + +
158C LEU* 1.3 75.4 - - - +
160C ASP* 1.3 66.6 + - - +
161C MET* 3.3 12.0 + - - +
177C PHE* 3.5 36.3 - - + -
178C ALA* 4.2 19.1 - - + +
181C PHE* 3.7 38.8 - - + -
182C TRP* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C HIS* 2.9 14.7 + - - -
76C HIS* 3.6 1.4 + - - -
79C TRP* 3.6 16.2 - - + -
125C TRP* 3.3 32.2 - - + -
159C LEU* 1.3 71.0 - - - +
161C MET* 1.3 58.7 + - - +
162C TRP* 2.8 41.6 + - - +
164C HIS* 3.4 0.3 + - - -
165C ALA* 3.5 16.8 - - + +
177C PHE* 3.4 23.7 - - - -
999C FE 2.0 31.0 - - - -
----------------------------------------------------------
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