Contacts of the helix formed by residues 133 - 148 (chain A) in PDB entry 3KAP
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 ASP 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS 5.4 0.5 - - - +
126A ILE* 3.5 22.2 - - + +
127A GLU 5.5 1.1 - - - +
129A ASP 3.9 1.2 + - - -
130A ALA 3.3 6.2 + - - -
131A SER 3.3 0.2 - - - -
132A SER* 1.3 86.3 + - - +
134A PRO* 1.3 66.2 - - - +
135A ASP* 3.2 7.1 + - - +
136A ALA* 3.2 33.2 + - - +
137A VAL* 3.4 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 6.5 0.9 - - + -
130A ALA 3.6 10.1 - - - +
131A SER* 3.8 12.8 - - - +
132A SER 3.7 6.3 - - - +
133A ASP* 1.3 89.6 - - - +
135A ASP* 1.3 69.4 + - - +
137A VAL* 3.4 6.4 + - + +
138A SER* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASP* 3.3 6.8 - - - +
134A PRO* 1.3 86.3 - - - +
136A ALA* 1.3 61.3 + - - +
138A SER* 3.7 7.0 + - - -
139A ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.7 11.5 - - + +
125A LYS 5.5 1.1 - - - +
126A ILE* 3.7 11.4 - - + -
133A ASP* 3.2 31.7 + - - +
135A ASP* 1.3 75.4 - - - +
137A VAL* 1.4 66.4 + - - +
139A ALA* 3.5 5.0 + - - +
140A PHE* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.8 7.0 - - + -
21A LYS* 3.7 32.3 - - + -
22A LEU* 3.8 21.3 - - + +
25A LEU* 4.7 1.8 - - + -
124A LEU* 4.2 14.1 - - + -
126A ILE* 3.5 16.8 - - + +
130A ALA* 4.0 24.0 - - + +
133A ASP 3.4 15.2 + - - +
134A PRO* 3.6 7.9 - - + +
136A ALA* 1.4 78.4 - - - +
138A SER* 1.3 61.9 + - - +
140A PHE* 3.3 2.6 + - - +
141A ALA* 3.0 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 5.4 4.0 - - - +
25A LEU* 4.1 19.6 - - - +
134A PRO* 2.8 23.5 + - - +
135A ASP* 3.7 8.0 + - - -
137A VAL* 1.3 75.4 - - - +
139A ALA* 1.3 56.6 + - - +
141A ALA* 3.3 3.8 + - - +
142A GLU* 3.0 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ASP 3.0 18.6 + - - +
136A ALA* 3.9 5.8 - - - +
138A SER* 1.3 72.8 - - - +
140A PHE* 1.3 60.6 + - - +
142A GLU* 3.3 15.8 + - - +
143A ASP* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.0 29.4 - - + -
54A LEU* 5.1 2.7 - - + -
89A ALA* 3.7 21.1 - - + -
90A ALA 3.5 18.8 - - - -
91A PHE* 4.4 4.9 - + + -
121A CYS* 3.8 16.6 - - - -
122A GLU 3.5 25.4 - - - -
123A GLY* 4.1 0.7 - - - -
124A LEU* 3.7 40.8 - - + -
136A ALA 3.0 17.9 + - - +
137A VAL 3.6 2.7 - - - +
139A ALA* 1.3 72.8 - - - +
141A ALA* 1.3 60.8 + - - +
143A ASP* 3.1 13.2 + - - +
144A VAL* 2.9 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.1 13.0 - - + -
25A LEU* 3.8 33.2 - - + -
26A VAL* 5.1 3.6 - - + -
137A VAL 3.0 13.3 + - - +
138A SER 3.3 8.7 + - - +
140A PHE* 1.3 74.5 - - - +
142A GLU* 1.3 53.0 + - + +
144A VAL* 3.1 15.6 + - + +
145A LEU* 2.8 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER* 3.0 32.2 + - - +
139A ALA* 3.3 15.3 + - - +
141A ALA* 1.3 77.4 - - + +
143A ASP* 1.3 62.4 + - - +
145A LEU* 3.4 10.4 + - + +
146A LYS* 3.3 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A CYS* 3.9 22.7 - - + +
122A GLU 5.7 0.3 - - - +
139A ALA* 2.9 24.9 + - - +
140A PHE* 3.1 17.4 + - - +
142A GLU* 1.3 76.6 - - - +
144A VAL* 1.4 60.3 + - - +
146A LYS* 3.6 9.4 + - - +
147A LYS* 3.4 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 6.1 0.4 - - + -
26A VAL* 3.8 27.8 - - + -
54A LEU* 4.7 15.3 - - + -
89A ALA* 4.6 6.7 - - + -
120A ILE* 4.3 14.1 - - + -
121A CYS* 4.3 8.3 - - - -
140A PHE* 2.9 43.2 + - + +
141A ALA* 3.1 13.0 + - - +
143A ASP* 1.4 75.3 - - - +
145A LEU* 1.3 63.6 + - - +
147A LYS* 2.9 18.5 + - - +
148A LEU* 3.0 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 21.1 - - + +
26A VAL* 3.9 24.7 - - + +
29A GLY* 4.3 12.8 - - - -
31A HIS* 3.6 34.4 + - + +
141A ALA* 2.8 22.2 + - + +
142A GLU* 3.7 10.8 - - + +
144A VAL* 1.3 76.9 - - - +
146A LYS* 1.3 59.8 + - + +
147A LYS 3.3 0.7 + - - -
148A LEU* 3.5 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 3.3 20.5 + - + +
143A ASP* 3.9 9.6 - - - +
145A LEU* 1.3 75.3 - - - +
147A LYS* 1.3 69.0 + - + +
148A LEU* 3.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 2.8 27.7 + - - +
120A ILE* 3.5 47.2 + - + +
121A CYS* 5.4 1.8 - - + -
143A ASP 3.4 14.8 + - - +
144A VAL 2.9 9.2 + - - +
146A LYS* 1.3 88.3 - - + +
148A LEU* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 4.3 15.9 - - - -
4A VAL* 3.8 22.2 - - + -
26A VAL* 4.1 9.4 - - + -
31A HIS* 3.7 42.4 - - + +
52A ALA* 3.7 28.9 - - + -
54A LEU* 5.8 3.4 - - + -
87A LYS* 3.6 23.1 + - + +
120A ILE* 5.5 4.7 - - + -
144A VAL* 3.0 29.2 + - + +
145A LEU* 3.5 15.5 + - + +
146A LYS 4.6 2.4 - - - +
147A LYS* 1.3 83.3 - - - +
----------------------------------------------------------
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