Contacts of the helix formed by residues 106 - 119 (chain A) 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 LEU 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 4.3 2.9 - - + -
104A ALA 3.6 5.4 + - - +
105A ASP* 1.3 73.3 + - - +
107A LYS* 1.3 63.6 + - - +
108A TYR 3.2 2.9 + - - -
109A ILE* 3.2 30.3 + - + +
110A GLU* 2.9 24.4 + - + +
133A PRO* 3.9 36.8 - - + -
135A ARG 5.6 0.7 - - - -
136A ALA* 4.1 15.7 - - + +
139A SER* 4.1 17.3 - - - +
323E PHE* 3.6 30.0 + - + +
325E THR* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 4.8 6.5 - - - -
96A TYR* 5.3 2.0 + - - -
105A ASP* 3.1 35.6 + - - +
106A LEU* 1.3 75.4 - - - +
108A TYR* 1.3 102.2 + - + +
110A GLU* 3.3 4.5 + - - +
111A ALA* 2.9 28.9 + - - +
325E THR* 3.8 14.4 - - - +
327E THR* 4.4 29.8 - - + +
329E LYS* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 3.6 21.1 - - + -
90A ASN* 3.4 46.2 - - - +
92A PRO* 4.0 13.0 - - + +
105A ASP 4.6 0.4 + - - -
106A LEU 3.3 0.8 - - - -
107A LYS* 1.3 112.5 + - + +
109A ILE* 1.3 66.8 + - - +
111A ALA* 3.3 8.0 + - + +
112A CYS* 3.0 27.5 + - - -
502A UPG 4.4 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 3.6 27.8 - - + +
89A VAL* 3.9 15.5 - - + +
91A THR* 3.5 26.9 - - + +
106A LEU* 3.2 23.4 + - + +
108A TYR* 1.3 78.5 - - - +
110A GLU* 1.3 59.0 + - - +
112A CYS* 3.3 5.1 + - - +
113A ALA* 3.0 25.5 + - - +
128A GLU* 5.7 2.7 - - + +
130A SER* 6.0 0.9 - - - -
132A VAL* 3.9 20.9 - - + -
136A ALA* 5.1 4.7 - - + +
139A SER* 6.1 2.0 - - - -
140A ILE* 3.8 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 2.9 17.6 + - + +
107A LYS* 3.6 5.0 - - - +
109A ILE* 1.3 75.8 - - - +
111A ALA* 1.3 66.8 + - - +
113A ALA* 3.1 2.3 + - - +
114A ARG* 2.8 64.2 + - - +
143A ILE* 3.7 17.9 - - + -
323E PHE* 3.5 19.4 - - + -
325E THR* 3.6 9.2 - - - +
329E LYS* 2.8 42.6 + - - -
409E HIS* 3.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS 2.9 17.2 + - - +
108A TYR* 3.3 10.5 + - + +
110A GLU* 1.3 78.5 - - - +
112A CYS* 1.3 62.8 + - - +
114A ARG* 3.3 7.6 + - - +
115A ARG* 2.9 25.4 + - - +
502A UPG 5.3 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.6 36.3 - - + -
87A ILE* 4.0 26.7 - - + -
89A VAL* 3.9 17.0 - - - -
108A TYR 3.0 17.3 + - - +
109A ILE 3.5 7.9 - - - +
111A ALA* 1.3 77.4 - - - +
113A ALA* 1.3 57.3 + - - +
115A ARG* 3.2 5.4 + - - +
116A ILE* 2.7 36.9 + - - +
502A UPG 4.4 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 4.6 2.9 - - + +
109A ILE 3.0 14.0 + - - +
110A GLU* 3.1 7.6 + - - +
112A CYS* 1.3 76.5 - - - +
114A ARG* 1.3 62.6 + - - +
116A ILE* 3.4 4.0 + - - -
117A VAL* 3.1 25.1 + - - +
140A ILE* 4.3 18.2 - - + -
143A ILE* 3.9 22.9 - - + -
144A PHE* 3.4 25.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU* 2.8 52.2 + - + +
111A ALA* 3.8 6.3 - - - +
113A ALA* 1.3 73.2 - - - +
115A ARG* 1.3 65.7 + - - +
117A VAL* 3.2 11.2 - - - +
118A GLN* 3.0 31.2 + - - +
143A ILE* 3.9 15.6 - - + +
147A ASN* 4.2 7.0 + - - +
323E PHE* 4.9 2.2 - - - -
409E HIS* 3.4 28.0 + - - -
433E LEU* 4.3 14.4 - - - +
434E LYS 2.7 36.6 + - - +
435E PRO* 4.2 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 5.6 1.1 - - + -
37A VAL* 4.3 11.9 - - - +
75A ILE* 3.5 38.7 - - + +
76A ASP* 2.9 33.6 + - - -
79A ILE* 3.7 19.1 - - + -
111A ALA 2.9 18.1 + - - +
112A CYS* 3.7 6.5 - - - +
114A ARG* 1.3 74.9 - - - +
116A ILE* 1.3 64.5 + - - +
118A GLN* 3.2 10.4 + - - -
119A ASN* 3.0 33.0 + - - +
502A UPG 5.3 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.9 18.2 - - + -
79A ILE* 4.1 14.6 - - + -
85A VAL* 3.7 28.0 - - + -
87A ILE* 4.0 13.5 - - + -
112A CYS 2.7 26.0 + - - +
113A ALA* 3.7 6.3 - - - +
115A ARG* 1.3 73.0 - - - +
117A VAL* 1.3 62.7 + - - +
119A ASN 3.2 1.0 + - - -
120A SER* 2.7 41.6 + - - +
126A VAL* 4.0 37.5 - - + -
144A PHE* 4.3 7.6 - - + -
154A LEU* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA 3.1 17.4 + - - +
114A ARG* 3.2 19.3 - - - +
116A ILE* 1.3 81.3 - - - +
118A GLN* 1.3 59.0 + - - +
119A ASN 3.3 0.5 + - - -
120A SER* 3.4 7.3 + - - +
143A ILE* 4.4 8.7 - - + -
144A PHE* 4.2 14.6 - - + +
147A ASN* 3.1 47.1 - - + +
149A LYS* 2.8 28.3 + - - -
152A LEU* 4.0 12.2 - - + +
154A LEU* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 3.0 24.6 + - - +
115A ARG* 3.2 11.1 + - - +
117A VAL* 1.3 78.8 - - - +
119A ASN* 1.3 65.4 + - - +
149A LYS* 3.3 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP* 3.0 52.7 + - - +
79A ILE* 4.0 15.3 - - + -
80A LYS* 3.5 31.6 - - + +
115A ARG* 3.0 35.8 + - - +
117A VAL 3.2 0.2 - - - -
118A GLN* 1.3 83.8 - - - +
120A SER* 1.3 60.7 + - - +
121A ASN* 5.4 2.1 + - - -
----------------------------------------------------------
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