Contacts of the strand formed by residues 109 - 118 (chain K) in PDB entry 2AK4
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 LEU 109 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K CYS* 4.0 18.2 - - + -
102K ASP 3.6 17.9 - - - +
103K LEU* 4.2 2.6 - - - +
107K GLY 4.1 0.4 + - - -
108K ARG* 1.3 89.9 - - - +
110K LEU* 1.3 63.3 + - - +
111K ARG* 3.7 25.8 - - - +
112K GLY 4.4 2.5 - - - +
130K LEU* 5.3 4.5 - - + -
160K LEU 4.0 8.5 - - - +
161K GLU* 3.8 36.8 - - + +
165K VAL* 4.0 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K SER* 5.4 3.6 - - - +
102K ASP* 2.8 26.6 + - + +
103K LEU 5.4 0.7 - - - -
104K GLY* 4.4 19.1 - - - +
108K ARG 3.5 0.8 + - - +
109K LEU* 1.3 79.2 - - - +
111K ARG* 1.3 71.5 + - + +
128K GLU* 4.9 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K CYS* 3.6 1.9 - - - -
102K ASP* 3.0 35.2 + - + +
109K LEU* 3.7 11.9 - - - +
110K LEU* 1.3 90.9 - - + +
112K GLY* 1.3 70.7 + - - +
113K HIS* 3.2 38.0 + - - +
126K LEU 5.1 4.9 + - - -
128K GLU* 2.8 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K GLY 3.6 6.7 - - - -
101K CYS* 4.6 1.1 - - - -
109K LEU* 4.4 3.6 - - - +
111K ARG* 1.3 92.2 + - - +
113K HIS* 1.3 65.5 + - - -
126K LEU 5.4 1.2 - - - +
127K ASN 5.2 0.5 - - - +
128K GLU* 5.2 3.3 + - - -
130K LEU* 4.0 27.4 - - - +
160K LEU* 4.1 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K ARG* 3.1 28.8 + - - +
98K MET* 5.0 1.3 - - + +
99K TYR* 3.2 5.8 - - - +
100K GLY 2.9 40.6 + - - +
102K ASP* 2.7 26.0 + - - -
111K ARG* 3.2 42.3 + - - +
112K GLY* 1.3 76.9 + - - -
114K ASP* 1.3 63.8 + - - +
115K GLN* 4.6 20.8 + - + +
126K LEU* 5.3 3.6 - - - -
130K LEU* 5.6 0.4 - - - -
160K LEU* 3.7 9.2 - - - +
58L LYS* 6.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K ARG* 2.8 38.7 + - - +
98K MET 3.5 5.2 - - - -
99K TYR* 3.7 6.7 - - + +
113K HIS* 1.3 77.3 - - - +
115K GLN* 1.3 64.3 + - - +
116K SER* 4.6 1.6 + - - -
124K ILE 4.4 0.3 - - - +
125K ALA* 3.6 1.6 - - - -
126K LEU* 2.9 49.4 + - + +
133K TRP* 4.6 3.9 - - - -
156K ARG* 2.5 40.5 + - - +
160K LEU* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K ARG* 3.5 2.8 - - - +
98K MET* 2.9 61.3 + - + +
113K HIS* 4.6 19.6 + - + +
114K ASP* 1.3 80.8 - - - +
116K SER* 1.3 63.7 + - - +
122K ASP* 4.9 5.2 - - - +
124K ILE 3.6 7.0 - - - +
125K ALA* 4.2 15.3 - - + +
126K LEU 5.9 0.9 - - - +
58L LYS 5.6 0.5 - - - +
60L TRP* 3.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K ILE* 5.1 0.2 - - - -
96K GLN 3.2 9.0 - - - -
97K ARG* 3.5 11.3 - - - +
114K ASP* 4.6 2.3 + - - -
115K GLN* 1.3 77.2 - - - +
117K ALA* 1.3 62.4 + - - +
122K ASP* 4.0 0.9 - - - +
123K TYR* 3.0 22.0 + - - -
124K ILE* 2.8 26.7 + - - +
147K TRP* 4.8 3.1 - - - -
156K ARG* 5.7 0.5 + - - -
60L TRP* 3.7 7.0 - - - -
13M TYR* 2.9 40.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81K LEU* 5.7 0.2 - - - +
94K ILE 4.5 0.2 - - - -
95K ILE* 3.4 9.9 - - - +
96K GLN* 2.8 35.1 + - + +
116K SER* 1.3 74.4 - - - +
118K TYR* 1.3 60.8 + - - +
120K GLY 4.6 1.1 - - - -
121K LYS 3.3 18.6 - - - +
123K TYR* 3.9 5.6 - - - -
60L TRP* 3.3 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K LEU* 4.7 5.4 + - + -
81K LEU* 3.5 37.7 - - + -
82K ARG* 4.2 8.1 + - - +
85K TYR* 3.5 39.0 - + - +
87K GLN* 2.6 28.2 + - - -
93K HIS* 3.2 29.5 - - + +
94K ILE 3.5 13.5 - - - -
95K ILE* 3.9 11.0 - - + -
117K ALA* 1.3 73.9 - - - +
119K ASP* 1.3 85.2 + - + +
120K GLY 3.2 1.3 - - - -
121K LYS* 2.9 24.6 + - - +
123K TYR* 3.8 15.3 - - + +
----------------------------------------------------------
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