Contacts of the strand formed by residues 141 - 151 (chain H) in PDB entry 1SY6
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 SER 141 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H GLY* 3.2 9.8 - - - -
140H SER* 1.3 84.7 + - - +
142H VAL* 1.3 59.8 + - - +
188H THR* 4.2 14.6 - - - +
189H VAL 3.1 20.9 - - - -
190H THR* 4.0 3.4 - - - -
191H SER* 3.5 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H PRO* 4.0 25.1 - - + -
141H SER* 1.3 76.3 - - - +
143H THR* 1.3 81.4 + - - +
144H LEU* 4.0 8.9 + - + +
187H VAL 3.8 0.9 - - - +
188H THR* 3.3 4.6 - - - +
189H VAL* 2.8 55.2 + - + +
190H THR 4.3 6.1 - - - +
191H SER* 4.6 4.7 - - - -
194H TRP* 4.0 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H PRO* 4.2 4.3 - - - +
142H VAL* 1.3 79.9 - - - +
144H LEU* 1.3 76.1 - - - +
186H SER* 4.2 14.4 - - - -
187H VAL 3.5 4.7 - - - +
188H THR* 3.0 25.3 + - - +
113L THR* 5.3 6.8 - - - +
115L SER* 3.9 20.7 + - - +
117L PHE* 3.3 30.1 - - + -
134L PHE* 4.3 2.5 - - + -
136L ASN* 4.3 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LEU 3.6 6.1 - - - +
132H PRO* 3.4 30.3 - - + -
142H VAL* 4.0 9.0 - - + +
143H THR* 1.3 78.6 - - - +
145H GLY* 1.3 59.8 + - - +
160H TRP* 4.9 0.2 - - + -
186H SER* 3.3 7.1 - - - -
187H VAL* 2.9 43.8 + - + +
189H VAL* 5.3 4.3 - - + -
194H TRP* 3.7 53.6 - - + +
199H ILE* 3.9 24.5 - - + -
216H ILE* 4.2 15.9 - - + -
117L PHE* 4.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LEU* 2.9 42.5 + - - +
144H LEU* 1.3 76.6 - - - +
146H CYS* 1.3 62.8 + - - +
160H TRP* 3.6 4.9 - - - -
185H SER 3.1 10.8 - - - -
216H ILE* 3.5 11.6 - - - +
117L PHE* 4.3 0.6 - - - -
134L PHE* 3.8 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H VAL* 3.8 23.1 - - - -
128H TYR 3.6 7.9 - - - -
129H PRO* 5.4 0.9 - - - -
130H LEU* 3.4 4.8 - - - +
145H GLY* 1.3 75.8 - - - +
147H LEU* 1.3 59.7 + - - +
148H VAL* 4.1 1.9 + - - -
158H LEU* 4.2 10.6 - - + +
160H TRP* 3.7 13.5 - - + -
184H SER* 3.3 6.8 - - - -
185H SER* 2.9 29.1 + - - +
201H CYS* 2.0 50.5 - - - -
203H VAL* 4.2 0.2 - - - -
214H LYS* 5.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H SER 3.4 2.4 - - - +
127H VAL* 3.4 4.2 - - - +
128H TYR* 2.8 60.7 + - + +
130H LEU* 3.9 17.2 - - + +
146H CYS* 1.3 74.2 - - - +
148H VAL* 1.3 60.7 + - - +
149H LYS* 3.8 12.1 + - + -
182H THR* 3.9 21.1 - - + -
183H LEU 3.8 11.7 - - - +
184H SER* 4.3 11.0 - - - -
123L GLN* 4.7 2.0 - - - +
130L SER* 3.8 31.0 - - - +
132L VAL* 4.2 12.8 - - + -
177L THR* 4.5 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H PRO* 3.7 27.1 - - + -
126H SER 3.4 4.3 - - - +
127H VAL* 4.5 4.3 - - + -
146H CYS* 4.7 1.1 - - - +
147H LEU* 1.3 74.8 - - - +
149H LYS* 1.3 58.0 + - - +
151H TYR* 3.8 14.4 - - + -
156H VAL* 4.6 6.7 - - + -
158H LEU* 3.8 9.0 - - + -
182H THR* 3.3 2.9 - - - -
183H LEU* 2.7 63.9 + - + +
203H VAL* 3.8 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H PRO* 3.7 0.7 - - - +
126H SER* 2.9 39.7 + - - +
128H TYR* 4.8 9.4 - - + -
147H LEU* 3.8 12.5 - - + -
148H VAL* 1.3 75.2 - - - +
150H GLY* 1.3 70.4 + - - +
151H TYR* 3.7 1.8 - - - -
181H TYR 3.6 1.3 - - - -
182H THR* 3.1 25.6 - - + +
123L GLN* 4.0 14.4 - - - +
129L ALA 5.8 0.2 - - - +
130L SER* 3.8 13.6 + - - +
179L THR* 3.2 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 150 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H THR* 3.4 10.7 - - - +
124H ALA 3.3 18.2 - - - +
126H SER 4.7 0.2 + - - -
149H LYS* 1.3 83.7 - - - +
151H TYR* 1.3 56.9 + - - -
180H LEU* 3.8 29.5 - - - +
181H TYR 2.8 12.8 + - - -
182H THR* 3.6 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 151 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H THR 3.3 11.9 - - - +
125H PRO* 3.3 37.5 - - + -
148H VAL* 3.8 26.2 - - + -
150H GLY* 1.3 73.2 - - - -
152H PHE* 1.3 65.2 + - - +
153H PRO 3.7 16.4 - - - -
154H GLU* 2.9 27.1 + - - -
156H VAL* 3.5 30.7 - - + +
174H ALA* 3.3 16.6 - - - +
180H LEU* 3.5 3.1 - - - +
181H TYR* 2.6 81.4 + + + +
182H THR* 4.1 1.6 - - - -
183H LEU* 3.9 4.8 - - + +
205H HIS* 3.9 2.7 - - + -
----------------------------------------------------------
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