Contacts of the strand formed by residues 191 - 199 (chain H) in PDB entry 1G9N
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 191 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H THR* 4.5 8.0 - - - +
125H THR* 3.6 20.5 - - + +
127H THR* 4.8 4.9 + - - -
159H ASP 3.3 4.2 + - - -
160H TYR* 3.0 58.1 + - + +
161H PHE* 3.3 32.2 - + - -
162H PRO* 4.4 4.5 - - + -
163H GLN* 4.0 34.1 - - + -
183H ALA* 4.1 4.3 - - + -
184H VAL* 3.1 10.1 - - - +
185H LEU* 3.5 46.3 - - + +
186H GLN* 4.0 1.1 - - - +
190H LEU* 1.3 74.8 - - - +
192H SER* 1.3 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 192 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H LEU* 4.8 5.5 - - - +
157H VAL 3.0 18.6 + - - -
158H LYS* 3.3 15.7 - - - +
160H TYR* 3.6 3.7 - - - -
183H ALA* 4.1 0.2 - - - -
184H VAL* 2.9 32.4 + - - +
186H GLN* 2.8 30.6 + - - -
191H TYR* 1.3 76.0 - - - +
193H LEU* 1.3 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H LEU* 3.9 1.2 - - - +
157H VAL* 3.1 53.6 + - + +
160H TYR* 4.0 4.6 - - + +
165H VAL* 3.3 37.2 - - + +
167H VAL* 4.4 9.6 - - + -
180H THR* 3.9 14.4 - - + -
181H PHE* 3.1 23.6 - - - +
182H PRO* 4.2 2.7 - - + -
183H ALA* 3.5 16.8 - - + +
192H SER* 1.3 80.0 + - - +
194H SER* 1.3 90.8 + - - +
195H SER 4.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H LEU* 5.7 0.4 - - - -
155H CYS 3.7 11.7 - - - -
156H LEU* 2.9 24.1 - - - +
180H THR* 3.4 0.6 - - - -
181H PHE* 2.8 56.9 + - - +
193H LEU* 1.3 94.6 + - - +
195H SER* 1.3 58.1 + - - +
196H VAL* 5.2 1.8 - - - -
135L VAL* 4.5 8.9 - - - +
178L SER* 4.5 9.6 + - - -
180L THR* 4.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H GLY* 4.1 0.7 - - - -
155H CYS* 2.8 37.7 + - - +
157H VAL* 5.5 1.3 - - - +
167H VAL* 3.1 25.6 - - - +
169H TRP* 3.0 29.1 + - - -
178H VAL* 5.0 0.7 - - - +
180H THR* 2.9 25.9 + - - +
193H LEU* 4.5 2.3 - - - +
194H SER* 1.3 72.3 - - - +
196H VAL* 1.3 71.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H LEU* 4.8 13.0 - - + -
152H ALA* 5.9 0.9 - - + -
153H LEU 3.2 14.4 - - - +
154H GLY* 3.8 4.0 - - - -
155H CYS 5.1 0.4 - - - +
169H TRP* 4.7 1.1 - - - -
178H VAL* 3.0 9.1 - - - +
179H HIS* 2.8 54.7 + - + +
181H PHE* 3.8 12.8 - - + -
194H SER* 4.9 2.0 - - - -
195H SER* 1.3 84.2 + - - +
197H VAL* 1.3 64.2 + - - +
198H THR* 5.7 1.1 - - - +
120L PHE* 5.1 1.1 - - + -
135L VAL* 5.9 1.3 - - + -
137L LEU* 3.4 37.2 - - + -
139L ASN* 4.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H ALA* 4.5 0.2 - - - -
153H LEU* 2.7 47.7 + - + +
169H TRP* 4.1 27.1 - - + -
174H LEU* 3.6 17.3 - - + -
176H SER 3.8 6.1 - - - +
177H GLY 3.0 19.3 - - - +
178H VAL* 3.4 17.3 - - + -
196H VAL* 1.3 79.6 - - - +
198H THR* 1.3 59.3 + - - +
199H VAL* 3.3 23.1 + - + -
209H TYR* 5.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 198 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H THR* 3.2 29.4 + - - +
151H ALA 3.7 16.2 - - - +
152H ALA* 3.3 18.9 - - + +
177H GLY* 3.5 11.3 + - - +
196H VAL* 5.7 0.9 - - - +
197H VAL* 1.3 70.0 - - - +
199H VAL* 1.3 62.8 + - - +
200H PRO* 4.8 0.2 - - - +
118L PHE* 4.5 8.5 - - + -
139L ASN* 3.2 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H THR* 3.3 5.6 - - - -
151H ALA* 2.6 36.8 + - - +
153H LEU* 3.5 22.7 - - + -
174H LEU* 3.5 35.4 - - + -
197H VAL* 3.5 14.8 - - + -
198H THR* 1.3 74.1 - - - +
200H PRO* 1.3 69.0 - - + +
201H SER* 3.5 0.3 + - - -
204H LEU* 5.0 2.2 - - + +
209H TYR* 3.2 34.8 - - + +
----------------------------------------------------------
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