Contacts of the strand formed by residues 150 - 158 (chain B) in PDB entry 4R7X
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 VAL 150 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 4.8 14.1 - - + +
78A GLU 3.4 8.1 - - - +
79A VAL* 4.3 16.4 - - + -
9B LEU* 4.5 16.1 - - + +
140B ALA 3.7 1.2 - - - +
141B GLU* 3.6 0.3 - - - -
142B LEU* 2.9 43.8 + - + +
144B ARG* 4.0 19.7 - - - +
148B LEU 3.5 11.9 - - - +
149B PRO* 1.3 78.1 - - - +
151B LYS* 1.3 71.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.4 4.4 - - - +
77A GLU* 3.3 8.2 - - - +
78A GLU* 2.8 63.9 + - + +
80A GLU* 2.6 35.3 + - + +
205A PO4 3.2 19.2 + - - -
9B LEU* 5.1 0.2 - - - -
139B LYS* 4.1 9.6 - - + +
140B ALA 3.2 5.6 - - - +
141B GLU* 3.5 33.0 - - + -
143B HIS* 5.4 0.9 - - - -
149B PRO* 5.2 6.7 - - + +
150B VAL* 1.3 85.7 - - - +
152B LEU* 1.3 60.4 + - - +
153B LYS* 4.3 0.7 - - + -
201B PO4 2.4 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP* 3.8 31.2 - - + -
75A TYR* 5.0 13.7 - - + -
76A THR 3.4 6.5 - - - +
77A GLU* 4.4 14.1 - - + +
9B LEU* 3.2 41.5 - - + +
10B THR* 3.7 16.8 - - + -
11B ILE* 3.5 31.2 - - + +
139B LYS* 3.1 4.3 - - - -
140B ALA* 2.8 36.4 + - + +
151B LYS* 1.3 73.8 - - - +
153B LYS* 1.3 62.7 + - - +
154B LYS* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 5.0 5.5 - - - +
74A ASN 3.9 0.5 - - - +
75A TYR* 3.4 7.4 - - - +
76A THR* 2.6 57.7 + - + +
78A GLU* 3.7 16.4 + - + +
201A PO4 5.4 0.4 + - - -
137B TRP* 3.6 43.9 - - + -
138B VAL 3.8 2.2 - - - -
139B LYS* 3.7 26.5 - - + +
151B LYS 4.3 0.2 - - - -
152B LEU* 1.3 73.9 - - - +
154B LYS* 1.3 61.3 + - - +
155B GLU* 4.2 0.6 + - + +
202B PO4 2.7 37.6 + - - +
203B PO4 3.5 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 5.0 3.4 - - - +
73A GLN* 3.4 28.3 - - - +
74A ASN 3.9 2.0 - - - -
75A TYR* 3.4 39.3 + - + -
11B ILE* 2.6 48.6 + - + +
12B SER* 4.2 7.1 - - - +
13B PHE* 3.8 33.6 - - + +
22B PRO* 5.8 0.2 - - - -
137B TRP* 3.2 2.3 - - - +
138B VAL* 2.9 37.9 + - - +
152B LEU* 3.9 1.9 + - + -
153B LYS* 1.3 72.9 - - - +
155B GLU* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 2.5 30.6 + - - +
74A ASN* 3.1 51.2 + - + +
13B PHE* 3.8 4.9 - - - -
126B SER* 5.6 5.2 + - - -
128B GLU* 3.9 11.3 - - - +
134B VAL 5.1 1.0 - - - +
135B ARG* 4.0 29.6 - - - +
136B TYR 3.2 15.7 - - - +
137B TRP* 3.8 7.0 - - + -
153B LYS* 4.2 1.0 + - + +
154B LYS* 1.3 73.3 - - - +
156B PHE* 1.3 70.9 + - - +
157B THR* 5.2 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.7 28.5 - + + -
22B PRO* 3.7 16.8 - - + +
24B TYR* 3.6 23.1 - + + -
30B VAL* 4.1 21.5 - - + -
51B ALA* 5.4 0.2 - - + -
52B ARG 5.1 0.9 - - - -
82B PHE* 5.2 3.1 - + - -
116B PHE* 4.6 6.1 - + - -
118B LEU* 4.5 10.5 - - + -
126B SER* 4.4 1.2 + - - -
136B TYR* 3.0 45.0 + + + +
137B TRP* 3.7 24.2 - - - -
138B VAL* 3.7 19.7 - - + -
155B GLU* 1.3 80.4 - - - +
157B THR* 1.3 61.1 + - - +
158B VAL* 3.5 26.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 6.1 0.9 - - - -
21B VAL* 5.9 1.6 - - - +
22B PRO* 2.9 16.0 + - - +
23B VAL* 3.3 21.4 - - + +
24B TYR* 2.8 26.5 + - - -
126B SER* 3.8 20.6 - - - +
155B GLU* 5.2 5.5 + - - +
156B PHE* 1.3 73.9 - - - +
158B VAL* 1.3 72.2 + - - +
159B PHE* 4.2 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.3 11.0 - - + +
25B SER* 4.7 3.6 - - - -
118B LEU* 4.0 12.6 - - + -
123B LEU* 4.1 23.8 - - + -
124B ALA 3.8 14.4 - - - +
125B THR* 3.5 2.6 - - - +
126B SER* 3.0 33.0 + - - -
136B TYR* 3.6 28.5 - - + -
156B PHE* 3.5 30.9 + - + -
157B THR* 1.3 74.1 - - - +
159B PHE* 1.3 67.9 + - - +
160B GLU* 4.9 2.5 - - - +
----------------------------------------------------------
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