Contacts of the strand formed by residues 120 - 126 (chain K) in PDB entry 2WWA
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 LYS 120 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85K GLN* 3.5 1.3 - - - -
86K VAL* 2.9 38.0 + - + +
87K SER 3.1 31.5 + - - +
88K MET* 3.1 25.8 + - - +
90K ALA* 3.8 17.9 + - + +
112K THR* 3.6 28.7 - - + +
113K LEU 3.3 23.3 - - - +
114K VAL* 4.6 11.2 - - + +
118K GLY 3.7 3.6 + - - +
119K THR* 1.4 69.3 - - - +
121K LYS* 1.4 65.0 + - - +
11O GLN* 5.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K ILE* 5.4 5.4 - - + -
83K VAL* 5.0 11.9 - - + -
84K PHE 3.5 11.7 - - - +
85K GLN* 4.3 8.1 - - + +
112K THR* 3.5 6.8 - - - +
113K LEU* 3.1 65.2 + - - +
114K VAL 3.2 23.3 + - - +
115K ARG* 4.7 20.9 - - + +
119K THR 3.5 5.1 + - - -
120K LYS* 1.4 72.6 - - - +
122K ALA* 1.4 58.6 + - - +
123K TYR* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K VAL* 3.4 8.2 - - - +
84K PHE* 2.9 34.8 + - + +
86K VAL* 4.1 18.6 - - + -
95K ILE* 4.1 24.2 - - + -
110K VAL* 5.3 0.7 - - + -
111K ASN 3.8 4.5 - - - -
112K THR* 3.9 15.5 - - + -
121K LYS* 1.4 74.9 - - - +
123K TYR* 1.3 60.5 + - - +
124K VAL* 3.8 6.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 123 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75K LYS* 3.6 34.9 - - + +
81K ILE* 3.5 40.4 - - + +
82K LEU 4.6 0.4 - - - -
83K VAL* 4.4 7.6 - - + -
109K LYS* 3.5 22.4 + - - +
110K VAL* 3.6 2.3 - - - +
111K ASN* 3.0 57.2 + - - +
121K LYS* 4.3 1.0 - - - +
122K ALA* 1.3 70.1 - - - +
124K VAL* 1.4 63.9 + - - +
125K ARG* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81K ILE* 3.5 4.3 - - - +
82K LEU 2.8 40.2 + - - +
84K PHE* 3.7 30.1 - - + -
95K ILE* 3.8 24.7 - - + -
99K VAL* 4.7 5.8 - - + -
107K VAL* 3.7 32.1 - - + -
109K LYS 3.6 2.7 - - - -
110K VAL* 4.9 3.6 - - + -
122K ALA* 4.0 7.4 - - + +
123K TYR* 1.4 78.2 - - - +
125K ARG* 1.4 62.4 + - - +
126K LEU* 3.5 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K GLY 4.3 5.2 - - - +
81K ILE* 4.0 30.3 - - + +
107K VAL* 3.5 8.5 - - - +
108K LEU* 3.0 64.0 + - + +
109K LYS* 3.2 37.1 + - + +
123K TYR* 4.1 4.9 - - + -
124K VAL* 1.4 73.7 - - - +
126K LEU* 1.4 70.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K GLY 3.9 9.0 - - - +
80K ASN 3.2 28.8 + - - +
82K LEU* 3.4 34.5 - - + +
99K VAL* 3.9 13.9 - - + -
105K VAL* 3.6 43.5 - - + -
106K ASP 3.8 6.1 - - - +
107K VAL* 4.7 0.4 - - + -
108K LEU* 3.6 14.5 - - - +
124K VAL* 3.5 15.3 - - + +
125K ARG* 1.4 78.4 - - - +
127K THR* 1.4 67.6 + - - +
128K ALA 3.9 0.2 + - - -
130K TYR* 3.7 29.2 - - + +
----------------------------------------------------------
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