Contacts of the strand formed by residues 156 - 163 (chain H) in PDB entry 4R2G
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 THR 156 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H SER 4.6 0.5 - - - -
133H PRO* 3.3 22.4 - - - +
155H GLY* 1.3 70.5 - - - -
157H TRP* 1.3 70.8 + - - +
158H THR* 3.9 8.7 + - - +
171H LYS* 4.6 16.4 - - + -
172H ILE 3.8 0.9 - - - +
173H ASP* 2.8 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 157 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H LEU* 3.9 26.0 - - + +
116H LEU* 5.2 5.8 - - + -
130H CYS* 4.7 12.8 - - + -
131H ARG 3.6 7.9 - - - -
132H SER* 3.4 37.9 - - - -
133H PRO* 3.5 10.5 - - + -
138H ILE* 4.3 17.3 - - + -
146H VAL* 4.3 20.6 - - + -
149H LEU* 4.9 9.8 - - + +
153H ASP* 3.3 30.5 + - + -
154H SER* 4.8 0.6 - - - +
155H GLY 3.7 13.1 - - - +
156H THR* 1.3 76.6 - - - +
158H THR* 1.3 62.4 + - - +
159H CYS* 4.0 9.2 - - - -
171H LYS* 3.5 5.2 - - - -
172H ILE* 2.9 42.1 + - + +
174H ILE* 3.8 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H GLN 3.9 1.7 - - - +
130H CYS* 3.6 0.5 - - - -
131H ARG* 2.9 61.3 + - - +
132H SER 5.7 0.2 + - - -
156H THR* 3.9 9.5 + - - +
157H TRP* 1.3 76.8 + - - +
159H CYS* 1.3 59.5 + - - +
160H THR* 3.8 4.0 + - - -
169H GLU* 3.1 30.3 - - - +
170H PHE 3.7 2.0 - - - -
171H LYS* 3.4 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 159 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H LEU* 3.5 21.3 - - + -
116H LEU* 3.7 16.8 - - - -
128H VAL* 4.6 1.6 - - + -
130H CYS* 2.0 55.6 - - - +
157H TRP* 4.0 7.6 - - - -
158H THR* 1.3 77.4 - - - +
160H THR* 1.3 62.4 + - - +
161H VAL 3.9 0.7 + - - -
168H VAL 3.9 0.9 - - - +
169H GLU* 4.6 1.1 - - - -
170H PHE* 2.9 42.7 + - - +
172H ILE* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H VAL* 3.5 1.4 - - - -
129H GLN* 2.9 53.7 + - - +
131H ARG* 5.9 1.6 + - - -
158H THR 4.3 2.9 + - - -
159H CYS* 1.3 72.2 - - - +
161H VAL* 1.3 64.0 + - - +
162H LEU* 5.8 0.7 - - + -
167H LYS* 3.6 42.2 - - + +
168H VAL 3.5 8.7 - - - +
169H GLU* 2.6 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 4.4 2.6 - - + +
98H PHE* 4.0 24.9 - - + -
100H LEU* 5.0 2.0 - - + -
118H LEU* 3.6 28.0 - - + -
126H PRO* 4.1 20.9 - - + -
127H SER 4.1 2.0 - - - -
128H VAL* 3.7 22.0 - - + -
159H CYS 4.9 0.7 - - - +
160H THR* 1.3 72.8 - - - +
162H LEU* 1.3 63.8 + - - +
163H GLN 4.2 0.2 + - - -
166H LYS 3.8 0.5 - - - +
167H LYS* 3.3 5.1 - - - -
168H VAL* 2.9 43.8 + - + +
170H PHE* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H SER 4.7 0.7 - - - +
126H PRO* 3.5 3.8 - - - +
127H SER* 2.9 49.9 + - - +
129H GLN* 4.4 20.9 - - - +
160H THR* 3.9 1.3 + - + -
161H VAL* 1.3 75.5 - - - +
163H GLN* 1.3 69.8 + - - +
164H ASN 5.0 0.2 - - - +
165H GLN* 4.4 10.3 - - - +
166H LYS 3.3 29.2 - - - +
167H LYS* 4.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 163 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 3.8 17.8 - - + +
96H LEU* 3.6 29.4 - - + +
98H PHE* 4.1 8.8 - - + -
124H SER* 3.5 12.4 - - - +
125H SER* 3.4 34.2 + - - +
126H PRO* 3.6 10.2 - - - +
162H LEU* 1.3 77.6 - - - +
164H ASN* 1.3 94.6 + - + +
165H GLN 3.4 2.0 - - - -
166H LYS* 3.0 25.9 + - - +
----------------------------------------------------------
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