Contacts of the helix formed by residues 132 - 141 (chain B) in PDB entry 5KYT
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 GLY 132 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B CYS* 5.5 4.9 - - - -
107B ASP 5.8 0.7 - - - -
114B LEU* 5.3 0.6 - - - +
128B VAL* 3.5 13.9 - - - -
129B SER* 2.9 10.3 + - - -
131B LYS* 1.3 82.0 - - - +
133B LEU* 1.3 65.5 - - - +
134B GLN 3.2 3.4 + - - -
135B LYS* 3.3 20.7 + - - +
136B ILE* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 4.2 7.9 - - + -
129B SER 3.4 7.5 + - - +
130B LYS* 3.2 15.1 + - - +
131B LYS 3.6 0.2 - - - -
132B GLY* 1.3 75.8 - - - +
134B GLN* 1.3 59.9 + - + +
136B ILE* 3.2 4.0 + - + +
137B LEU* 2.9 47.7 + - + +
149B ILE* 4.0 20.2 - - + -
151B ILE* 3.9 19.7 - - + -
158B TYR* 4.0 17.5 - - + -
159B GLN* 3.6 24.7 - - + +
161B PHE* 4.1 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS 4.9 0.6 + - - -
131B LYS 5.1 1.9 + - - +
132B GLY 3.3 1.0 - - - -
133B LEU* 1.3 79.7 - - + +
135B LYS* 1.3 59.4 + - + +
137B LEU* 3.1 25.3 + - - +
138B ASN* 2.9 58.6 + - - +
159B GLN* 5.6 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASP 3.2 26.7 + - - -
108B ILE* 4.5 2.6 - - - +
109B TYR 3.6 23.9 + - - +
110B ASN* 4.9 1.3 - - - -
111B GLU* 3.8 31.5 - - + +
114B LEU* 3.6 20.1 - - + +
131B LYS* 4.3 10.3 + - - +
132B GLY* 3.3 22.6 + - - +
134B GLN* 1.3 78.9 - - + +
136B ILE* 1.3 62.9 + - - +
138B ASN* 3.3 3.5 + - - +
139B VAL* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B CYS* 4.6 11.0 - - + -
114B LEU* 4.0 19.3 - - + -
118B MET* 3.8 27.8 - - - -
126B VAL* 3.9 24.9 - - + -
128B VAL* 3.7 21.1 - - + -
132B GLY 3.2 12.4 + - - +
133B LEU* 3.5 9.2 - - - +
135B LYS* 1.3 76.6 - - - +
137B LEU* 1.3 57.6 + - - +
139B VAL* 3.2 5.3 + - + +
140B GLN* 2.8 29.1 + - + +
146B ILE* 5.5 2.8 - - + +
149B ILE* 3.5 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 2.9 37.6 + - + +
134B GLN* 3.1 31.2 + - - +
136B ILE* 1.3 74.7 - - - +
138B ASN* 1.3 66.7 + - - +
139B VAL 3.2 0.7 + - - -
140B GLN* 3.2 24.8 + - - +
141B LYS* 4.0 5.2 + - - +
149B ILE* 3.7 19.3 - - + -
159B GLN* 5.8 0.7 - - - +
161B PHE* 3.5 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLU* 2.3 48.5 + - + +
134B GLN* 2.9 40.3 + - - +
135B LYS 3.6 5.8 - - - +
137B LEU* 1.3 78.7 - - - +
139B VAL* 1.3 60.4 + - + +
141B LYS* 4.2 10.2 + - - +
142B LYS* 4.9 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLU* 3.6 32.5 - - + +
114B LEU* 4.3 9.6 - - + +
115B LEU* 3.8 39.0 - - + +
118B MET* 5.0 10.1 - - - -
135B LYS 3.1 18.9 + - - +
136B ILE* 3.8 6.3 - - - +
137B LEU 3.2 0.2 - - - -
138B ASN* 1.3 75.9 - - + +
140B GLN* 1.3 68.5 + - - +
142B LYS* 3.0 22.5 + - - +
143B LEU* 3.6 14.8 + - + -
146B ILE* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE 2.8 21.6 + - - +
137B LEU* 3.2 18.7 + - - +
139B VAL* 1.3 73.6 - - - +
141B LYS* 1.3 60.0 + - - +
143B LEU 2.8 28.6 + - - +
144B PRO* 4.9 0.3 - - - +
146B ILE* 3.5 49.5 + - + +
147B GLN 4.9 5.5 - - - -
148B LYS* 5.6 0.2 - - - +
149B ILE* 3.7 25.9 - - + +
161B PHE* 5.5 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU 4.0 5.1 + - - +
138B ASN 4.5 8.3 - - - +
139B VAL 3.1 1.2 + - - -
140B GLN* 1.3 80.8 - - - +
142B LYS* 1.3 61.0 + - + +
143B LEU 3.6 0.3 + - - -
144B PRO* 4.7 7.3 - - - +
----------------------------------------------------------
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