Contacts of the strand formed by residues 143 - 151 (chain A) in PDB entry 2V9R
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 GLY 143 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 4.3 7.6 - - - -
141A ASP 3.5 2.6 + - - -
142A GLU* 1.3 74.6 - - - +
144A VAL* 1.3 64.6 + - - -
145A TYR* 3.3 10.3 - - - -
162A SER* 4.4 2.2 - - - -
163A LEU 2.9 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR 3.6 0.5 - - - +
103A LYS* 3.3 5.3 - - - +
104A GLY* 3.0 31.4 + - - +
143A GLY* 1.3 74.1 - - - -
145A TYR* 1.3 63.1 + - - +
160A ASP* 3.4 37.2 - - + +
161A ALA 3.5 7.6 - - - +
162A SER* 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 4.5 0.7 - - - +
87A LEU* 3.5 27.8 - - + -
101A TRP* 4.2 16.8 - + + -
102A TYR 3.2 13.9 - - - -
103A LYS* 3.3 29.2 - - + +
108A VAL* 3.9 14.8 - - + +
119A ARG* 5.0 1.0 + - - -
127A LEU* 4.0 3.8 - - + -
129A PHE* 3.4 28.7 - + - -
140A PRO 4.1 0.3 + - - -
141A ASP* 2.5 36.7 + - - -
143A GLY 3.3 23.8 - - - -
144A VAL* 1.3 76.4 - - - +
146A VAL* 1.3 61.5 + - - +
159A HIS 4.0 0.9 - - - +
160A ASP* 3.2 8.2 - - - -
161A ALA* 2.7 39.2 + - + +
163A LEU* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 5.1 0.2 - - - -
100A GLU 4.0 0.2 - - - +
101A TRP* 3.5 7.7 - - - -
102A TYR* 3.0 43.8 + - + +
145A TYR* 1.3 78.5 - - - +
147A CYS* 1.3 58.9 + - - +
148A VAL* 4.0 10.8 - - + -
157A VAL* 3.6 23.6 - - + -
158A SER* 3.3 31.9 - - - +
159A HIS 3.7 8.1 - - - +
160A ASP* 3.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 4.4 2.6 - - - +
72A GLU 4.7 0.4 - - - -
74A PRO* 4.2 5.4 - - - -
89A CYS* 2.0 55.0 - - + -
99A ILE* 4.1 5.6 - - + -
100A GLU 3.4 5.8 - - - +
101A TRP* 3.7 20.6 - - + -
146A VAL* 1.3 75.2 - - - +
148A VAL* 1.3 60.5 + - - +
149A ALA 4.4 0.4 - - - -
156A ALA 4.3 0.2 - - - +
157A VAL* 3.6 1.4 - - - +
158A SER* 2.8 53.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 5.1 0.2 - - - -
98A THR 3.6 0.7 - - - +
99A ILE* 3.5 3.6 - - - -
100A GLU* 2.8 35.4 + - - +
102A TYR* 3.7 24.7 - - + -
146A VAL* 4.0 3.1 - - + -
147A CYS* 1.3 79.2 - - - +
149A ALA* 1.3 68.7 + - - +
150A ARG* 3.7 37.1 + - + +
155A GLU* 4.4 8.7 - - + -
156A ALA 3.3 11.7 - - - +
157A VAL* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 3.7 15.8 - - + +
70A ILE* 4.1 8.6 - - + +
91A ALA* 3.5 32.3 - - + -
97A PRO* 4.0 2.5 - - + -
98A THR 3.2 6.7 - - - +
99A ILE* 3.8 8.5 - - + -
147A CYS 4.4 0.2 - - - -
148A VAL* 1.3 73.0 - - - +
150A ARG* 1.3 61.8 + - - +
155A GLU* 3.1 5.9 - - - +
156A ALA* 2.8 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PRO* 3.8 4.3 - - - -
96A THR 4.5 0.2 - - - +
97A PRO* 3.2 4.0 - - - +
98A THR* 2.9 41.5 + - - +
100A GLU* 2.6 39.0 + - - +
102A TYR* 3.2 28.6 + - - -
148A VAL* 3.7 28.1 + - + +
149A ALA* 1.3 80.3 - - - +
151A ASN* 1.3 63.8 + - - +
154A GLY 3.4 5.2 - - - +
155A GLU* 4.1 15.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE 2.9 25.7 + - - -
68A PRO* 3.4 22.9 - - - +
93A GLY* 4.1 1.8 - - - -
94A ARG 3.4 8.9 + - - +
95A PRO* 3.0 40.3 + - + +
96A THR 4.6 1.3 - - - +
97A PRO* 4.4 2.2 - - + -
150A ARG* 1.3 76.9 - - - +
152A TYR* 1.3 66.3 + - - +
153A LEU* 3.1 18.8 + - - +
154A GLY* 3.0 19.8 + - - +
----------------------------------------------------------
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