Contacts of the strand formed by residues 122 - 128 (chain A) in PDB entry 4NAK
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 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 4.2 4.7 + - - +
79A VAL* 3.6 14.4 - - + +
81A VAL* 3.8 25.8 - - + -
116A PHE* 3.5 28.7 - - + +
119A MET* 3.0 21.2 + - + +
120A PRO 3.9 3.1 - - - +
121A GLU* 1.3 78.5 - - + +
123A LYS* 1.3 61.5 + - - +
124A GLU 3.5 25.4 - - - +
125A ILE* 4.2 4.0 - - + -
145A ASP 4.8 1.4 - - - +
146A VAL* 3.4 16.3 - - + +
176A CYS* 6.4 0.2 - - - -
194A LEU* 5.0 3.8 - - + -
412A K 3.3 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 3.4 50.2 + - + +
78A SER 4.8 0.7 - - - -
79A VAL 2.8 17.5 + - - +
80A SER* 5.1 0.7 - - - +
121A GLU 3.4 2.4 + - - -
122A VAL* 1.3 72.7 - - - +
124A GLU* 1.3 71.9 + - + +
146A VAL* 3.8 4.3 - - - -
147A ASP* 3.1 44.0 + - - +
169A ASP* 3.0 33.7 + - + +
172A SER* 5.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL 3.6 0.4 + - - -
80A SER* 2.7 27.2 + - - +
81A VAL 2.9 24.3 + - - -
122A VAL* 3.5 10.0 - - - +
123A LYS* 1.3 88.9 + - + +
125A ILE* 1.3 65.3 + - - +
126A VAL* 4.8 8.7 - - + -
146A VAL* 4.2 1.6 - - - -
147A ASP* 3.2 25.9 - - + +
149A SER* 5.0 7.3 + - - +
167A GLU 4.6 3.0 - - - +
168A ILE* 3.2 9.5 - - - -
169A ASP* 2.5 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.6 19.3 - - + -
83A LEU* 4.1 18.8 - - + -
113A PHE* 3.5 45.8 - - + +
116A PHE* 4.0 6.7 - - + -
117A SER* 4.0 11.4 - - - +
122A VAL* 4.2 5.4 - - + -
124A GLU* 1.3 78.5 - - - +
126A VAL* 1.3 62.5 + - - +
127A VAL* 3.6 21.4 + - + -
146A VAL* 3.7 22.7 - - + -
147A ASP 2.8 11.3 + - - +
148A LEU* 3.6 6.5 - - + +
149A SER 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 5.5 0.2 - - - -
81A VAL 2.7 16.3 + - - +
82A ILE* 3.5 6.4 - - + -
83A LEU 2.9 25.2 + - - -
124A GLU* 4.6 9.4 - - + +
125A ILE* 1.3 72.8 - - - +
127A VAL* 1.3 62.8 + - - +
128A VAL* 3.6 2.3 + - - +
149A SER* 3.5 21.5 - - - +
150A PHE 4.5 0.7 - - - -
151A ALA* 4.0 13.5 - - + +
164A GLY* 3.7 28.9 - - - +
167A GLU* 3.8 21.5 - - + +
168A ILE* 4.1 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.7 11.9 - - + +
85A ALA* 4.5 3.6 - - + -
113A PHE* 3.9 20.2 - - + -
125A ILE* 4.0 8.3 - - + -
126A VAL* 1.3 70.4 - - - +
128A VAL* 1.3 63.1 + - - +
129A CYS* 3.7 18.8 + - + -
137A PHE* 3.8 37.7 - - + -
148A LEU* 3.8 24.2 - - + -
149A SER 2.9 7.7 + - - -
150A PHE* 3.4 15.9 - - + -
151A ALA 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 3.8 28.5 - - + -
83A LEU 2.9 13.4 + - - +
84A LEU* 4.2 7.4 - - + -
85A ALA* 2.9 29.6 + - - -
86A GLY 3.0 6.1 + - - +
126A VAL 4.2 2.0 - - - +
127A VAL* 1.3 71.5 - - - +
129A CYS* 1.3 60.5 + - - +
151A ALA* 3.4 10.1 - - + +
152A ILE 4.0 2.9 - - - +
153A PRO* 3.7 32.3 - - + -
160A SER* 3.8 30.3 - - - +
164A GLY* 4.0 12.8 - - - -
----------------------------------------------------------
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