Contacts of the strand formed by residues 126 - 135 (chain D) in PDB entry 3PJV
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 GLU 126 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D SER* 3.4 1.2 - - - -
123D ARG* 2.8 50.0 + - + +
125D TRP* 1.3 80.2 - - - +
127D GLN* 1.3 78.3 + - - +
128D ALA* 3.3 1.0 + - - +
85F LYS* 3.0 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LEU* 3.6 39.1 - - + +
121D VAL 3.8 1.8 - - - +
122D SER* 2.7 27.5 + - - +
125D TRP 3.8 9.7 - - - +
126D GLU* 1.3 87.8 - - - +
128D ALA* 1.3 59.5 + - - +
129D ALA 3.8 0.2 - - - -
84F LEU* 3.9 27.8 - - + +
85F LYS* 5.3 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D VAL 2.7 15.6 + - - +
122D SER 4.3 1.1 - - - -
123D ARG* 3.6 57.0 + - + +
126D GLU* 3.3 1.5 + - - +
127D GLN* 1.3 74.1 - - - +
129D ALA* 1.3 59.9 + - - +
57F ILE* 4.5 10.5 - - + -
83F ASP* 3.7 9.7 - - - +
84F LEU* 3.0 21.7 + - - -
85F LYS* 4.3 2.7 + - - +
90F ILE* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LEU* 3.5 3.5 - - - -
121D VAL* 2.8 37.4 + - + +
128D ALA* 1.3 79.6 - - - +
130D ARG* 1.3 59.7 + - - +
57F ILE* 4.2 20.2 - - + -
81F VAL* 4.0 19.7 - - + -
82F VAL 3.1 15.0 - - - +
84F LEU* 3.7 10.4 - - - +
90F ILE* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ASP* 4.1 21.9 + - + -
119D ALA 3.5 8.5 - - - +
120D LEU* 3.9 17.9 - - + +
129D ALA* 1.3 73.7 - - - +
131D VAL* 1.3 71.7 + - - +
132D GLU* 2.8 30.8 + - + +
80F ARG* 3.6 5.2 - - - +
81F VAL* 3.4 4.4 - - - -
82F VAL* 2.9 54.1 + - + +
84F LEU* 3.5 31.4 - - + +
87F ASP* 4.7 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D GLY 4.0 0.2 - - - +
118D ASP* 3.0 27.4 - - - +
119D ALA 2.8 14.7 + - - +
121D VAL* 3.9 17.3 - - + -
130D ARG* 1.3 73.4 - - - +
132D GLU* 1.3 62.6 + - - +
133D VAL* 4.1 15.3 - - + -
46F ALA* 4.0 13.4 - - - +
49F LEU* 3.7 28.5 - - + -
50F ALA* 4.0 10.8 - - - +
53F LEU* 3.8 27.6 - - + -
79F ILE* 4.5 2.0 - - + -
80F ARG 3.5 6.7 - - - +
81F VAL* 4.4 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D GLY 3.7 4.5 - - - +
118D ASP* 4.1 6.7 - - + +
130D ARG* 2.8 47.8 + - + +
131D VAL* 1.3 76.3 - - - +
133D VAL* 1.3 63.2 + - - +
134D VAL* 5.6 2.9 - - + -
78F SER* 4.0 1.3 + - - +
79F ILE* 3.3 5.0 - - - +
80F ARG* 2.7 84.6 + - + +
82F VAL* 4.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D GLY* 3.3 4.0 - - - -
117D GLY 2.8 33.9 + - - +
131D VAL* 4.1 9.4 - - + -
132D GLU* 1.3 78.3 - - - +
134D VAL* 1.3 67.5 + - - +
42F ALA* 3.5 26.0 - - + +
45F ALA* 4.2 4.7 - - + +
46F ALA* 3.7 28.0 - - - +
49F LEU* 5.1 1.1 - - + -
76F TYR* 3.6 35.0 - - + -
78F SER 3.6 5.2 - - - +
79F ILE* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D PRO* 3.8 32.8 - - + +
116D GLY* 4.1 13.9 - - - +
132D GLU* 5.6 2.9 - - + -
133D VAL* 1.3 82.6 - - - +
135D SER* 1.3 59.5 + - - +
137D PRO* 6.1 0.2 - - + -
76F TYR* 3.5 3.8 - - - +
77F SER* 2.8 44.1 + - - +
78F SER* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D TYR* 5.0 0.7 - - - -
114D PRO 4.6 6.7 + - - +
134D VAL* 1.3 80.3 - - - +
136D HIS* 1.3 65.5 + - - +
137D PRO* 3.4 7.4 - - - +
38F LEU* 3.1 44.4 + - - +
41F HIS* 2.8 30.5 + - - -
42F ALA* 3.2 14.5 + - - +
75F TYR 4.0 3.8 - - - -
76F TYR* 4.3 3.5 - - - +
77F SER* 3.7 3.3 + - - -
----------------------------------------------------------
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