Contacts of the helix formed by residues 135 - 147 (chain B) in PDB entry 3KHU
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 ARG 135 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A THR* 6.0 3.4 - - + -
106B LEU* 5.7 1.3 - - - -
134B VAL* 1.3 89.0 + - + +
136B ALA* 1.3 65.3 + - - +
137B ALA 3.3 2.0 - - - -
138B GLU* 3.2 40.1 + - - +
139B SER* 3.2 15.3 + - - +
214B TRP* 4.8 13.6 - - + +
217B GLU* 2.8 11.3 + - - -
286B TYR* 5.2 6.7 - - - -
287B LEU* 3.7 25.3 - - - +
290B ALA* 4.1 20.0 + - - +
291B LEU* 3.6 24.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 4.3 21.5 - - + -
109B ILE* 5.2 4.3 - - + +
128B GLU* 3.0 19.3 - - - +
132B VAL* 3.6 18.2 - - + -
133B PRO* 3.2 19.8 + - - +
134B VAL 3.4 0.8 + - - -
135B ARG* 1.3 76.3 - - - +
137B ALA* 1.3 62.2 + - - +
139B SER* 2.9 19.7 + - - -
140B ILE* 3.1 14.3 + - - +
217B GLU* 3.5 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 3.0 14.5 + - - +
135B ARG 3.3 0.2 - - - -
136B ALA* 1.3 72.6 - - - +
138B GLU* 1.3 56.1 + - - +
140B ILE* 3.3 5.6 + - - +
141B ARG* 2.9 29.5 + - - +
156B VAL* 4.0 19.5 - - + +
158B SER* 5.5 0.2 - - - -
213B THR* 3.4 28.0 - - + -
217B GLU* 2.8 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 3.2 38.2 + - - +
136B ALA 3.2 0.4 - - - -
137B ALA* 1.3 79.0 - - - +
139B SER* 1.3 59.1 + - - +
141B ARG* 3.4 8.1 + - - +
142B ARG* 3.0 62.9 + - + +
214B TRP* 4.3 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 4.2 12.4 - - - +
109B ILE* 6.1 2.0 - - - -
135B ARG* 3.2 11.5 + - - +
136B ALA* 2.9 12.7 + - - -
138B GLU* 1.3 74.1 + - - +
140B ILE* 1.3 67.0 + - - +
142B ARG* 3.1 4.8 + - - +
143B ILE* 3.1 30.0 + - - +
323D PHE* 3.2 44.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 4.1 13.7 - - + -
109B ILE* 3.8 29.2 - - + -
113B ALA* 4.2 16.6 - - + -
126B VAL* 4.7 6.3 - - + -
128B GLU* 3.7 36.1 - - + +
136B ALA 3.1 7.3 + - - +
137B ALA* 3.5 8.1 - - - +
139B SER* 1.3 76.4 - - - +
141B ARG* 1.3 62.2 + - - +
143B ILE* 3.1 6.3 + - + +
144B PHE* 3.0 55.1 + - + -
156B VAL* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA 2.9 17.0 + - - +
138B GLU* 3.6 9.4 - - - +
140B ILE* 1.3 78.0 - - - +
142B ARG* 1.3 57.4 + - + +
144B PHE* 3.4 25.8 + - - +
145B ASP* 2.9 67.5 + - - +
154B LEU* 2.8 34.6 + - - +
155B GLN* 4.2 10.1 + - - +
156B VAL* 4.0 22.2 - - + +
183B ASP* 5.4 8.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 3.0 48.5 + - + +
139B SER* 3.1 8.4 + - - +
141B ARG* 1.3 73.9 - - + +
143B ILE* 1.3 66.3 + - - +
145B ASP* 3.4 6.9 + - + +
146B ALA* 3.0 27.1 + - - +
320D ASP 5.8 1.6 + - - -
321D SER* 5.3 5.5 + - - +
323D PHE* 4.1 30.6 - - + -
435D PRO* 4.6 7.9 - - + +
458D GLN* 5.6 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 3.7 33.2 - - + +
113B ALA* 3.9 29.6 - - + +
114B ARG* 3.9 33.7 - - + +
117B VAL* 4.4 4.3 - - + -
139B SER* 3.1 18.7 + - - +
140B ILE* 3.6 5.8 - - + +
142B ARG* 1.3 76.2 - - - +
144B PHE* 1.3 62.6 + - + +
146B ALA* 3.3 2.3 + - - -
147B ASN* 2.8 44.1 + - - +
323D PHE* 3.9 19.5 - - + -
435D PRO* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 3.4 36.1 - - + -
116B ILE* 4.3 6.7 - - + -
117B VAL* 4.2 9.7 - - + +
126B VAL* 3.9 23.3 - - + -
140B ILE* 3.0 34.4 + - + -
141B ARG* 3.6 22.0 - - - +
143B ILE* 1.3 79.4 - - + +
145B ASP* 1.3 62.3 + - - +
147B ASN* 3.1 21.6 + - - -
148B THR* 3.6 5.4 + - - -
152B LEU* 5.8 2.1 - - + +
154B LEU* 3.7 44.9 - - + -
156B VAL* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG* 2.9 58.9 + - - +
142B ARG* 3.9 7.7 - - - +
144B PHE* 1.3 73.8 - - - +
146B ALA* 1.3 60.6 + - - +
147B ASN 3.6 0.3 + - - -
148B THR* 4.1 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG 3.0 17.9 + - - +
143B ILE 3.8 4.0 - - - +
144B PHE 3.2 0.2 - - - -
145B ASP* 1.3 76.7 - - - +
147B ASN* 1.3 58.6 + - - +
148B THR 3.6 1.7 + - - -
434D LYS* 3.5 20.0 - - + +
435D PRO* 3.6 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG* 4.2 5.1 + - - +
117B VAL* 3.1 38.5 - - + +
143B ILE* 2.8 33.6 + - - +
144B PHE 3.1 6.8 + - - +
146B ALA* 1.3 79.6 - - - +
148B THR* 1.3 64.2 + - - +
149B LYS* 3.9 3.3 + - - +
152B LEU* 4.4 1.2 - - - +
434D LYS* 3.0 41.4 + - - +
----------------------------------------------------------
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