Contacts of the helix formed by residues 109 - 123 (chain B) in PDB entry 3ZQI
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 GLN 109 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 3.4 22.2 - - + +
60B LEU* 5.6 2.0 - - + -
67B PHE* 4.2 17.0 - - + -
105B PRO* 3.8 18.4 - - + -
106B THR* 2.7 44.6 + - - +
108B LYS* 1.4 81.9 - - - +
110B TYR* 1.3 63.6 + - - +
111B GLU 3.3 2.9 - - - -
112B THR* 3.1 14.9 + - - -
113B LEU* 3.1 17.0 + - + +
1205B EDO 3.0 28.7 + - - -
1206B EDO 2.8 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASP* 2.6 31.2 + - - -
165A SER 3.4 24.5 - - - -
166A MET* 3.9 12.3 - - + -
167A PRO* 3.6 25.4 - - + +
170A LEU* 3.7 13.6 - - + +
104B ARG* 2.8 23.8 + - - -
105B PRO 4.3 0.7 - - - -
106B THR 3.3 16.6 - - - -
107B GLU* 3.1 34.6 + - + +
109B GLN* 1.3 80.2 - - - +
111B GLU* 1.3 56.9 + - - +
113B LEU* 3.2 3.0 + - + +
114B GLU* 2.8 31.9 + - - +
13D MET* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PRO* 5.4 1.1 - - - -
107B GLU 4.6 2.0 + - - -
108B LYS 4.8 4.6 + - - +
109B GLN 3.3 0.4 - - - -
110B TYR* 1.3 78.1 - - - +
112B THR* 1.3 65.1 + - - +
114B GLU* 3.4 6.3 + - + +
115B ASN* 2.9 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 3.5 49.1 - - + +
68B SER* 3.6 24.7 + - - +
108B LYS 5.1 0.4 + - - -
109B GLN* 3.1 11.0 + - - -
111B GLU* 1.3 80.6 - - - +
113B LEU* 1.4 62.8 + - - +
115B ASN* 3.2 8.0 + - - +
116B GLN* 3.0 22.1 + - - +
1206B EDO 3.8 21.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 4.1 20.9 - - + -
67B PHE* 4.0 15.5 - - + -
105B PRO* 4.0 17.9 - - + -
109B GLN* 3.1 17.5 + - + +
110B TYR* 3.8 4.5 - - - +
112B THR* 1.4 75.2 - - - +
114B GLU* 1.3 62.0 + - - +
116B GLN* 3.2 15.4 + - - +
117B LEU* 3.1 26.7 + - - +
13D MET* 3.6 34.1 - - + -
14D TRP* 3.5 34.8 - - + +
16D TRP* 3.9 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PRO* 3.3 27.3 - - + +
168A PRO* 3.3 13.3 - - - +
169A LEU* 2.9 37.1 + - + +
170A LEU* 2.8 29.3 + - - +
110B TYR 2.8 21.2 + - - +
111B GLU* 3.7 6.7 - - + +
113B LEU* 1.3 70.8 - - - +
115B ASN* 1.3 62.0 + - - +
117B LEU* 3.2 7.1 + - - +
118B ALA* 2.8 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B SER* 5.4 6.5 + - - +
69B PRO* 4.4 9.4 - - + +
111B GLU* 2.9 40.7 + - - +
112B THR* 3.2 7.8 + - - +
114B GLU* 1.3 80.0 - - - +
116B GLN* 1.4 58.4 + - - +
118B ALA* 3.8 8.0 - - - +
119B PHE* 2.9 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 2.9 29.6 - - - +
69B PRO* 4.3 11.6 - - + +
78B PHE* 4.0 11.7 - - + -
82B ASN* 3.9 3.6 + - - -
112B THR 3.0 19.2 + - - +
113B LEU* 3.2 15.7 + - - +
115B ASN* 1.4 74.2 - - - +
117B LEU* 1.4 59.0 + - - +
119B PHE* 3.6 1.4 - - - +
120B LEU* 2.9 35.4 + - - +
134B LEU* 3.7 20.8 - - + +
14D TRP* 2.8 36.4 - - - +
16D TRP* 2.9 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 3.5 45.8 - - + +
170A LEU* 3.6 12.1 - - + +
173A ALA* 4.0 5.8 - - + -
113B LEU 3.1 12.8 + - - +
114B GLU* 3.2 6.0 + - - +
116B GLN* 1.4 73.8 - - - +
118B ALA* 1.3 65.1 + - - +
120B LEU* 4.2 3.0 - - - +
121B THR* 2.8 32.7 + - - +
127B LEU* 4.1 15.5 - - + -
130B ALA* 4.3 11.4 - - + -
131B LEU 4.3 6.3 - - - +
134B LEU* 3.7 23.1 - - + -
14D TRP* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 3.8 13.2 - - + +
114B GLU* 2.8 18.7 + - + +
115B ASN* 3.8 12.6 - - - +
117B LEU* 1.3 75.4 - - - +
119B PHE* 1.3 58.7 + - - +
121B THR* 3.1 7.4 + - - -
122B GLN* 2.9 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 3.5 31.2 - - + -
70B LEU 5.3 2.7 - - - -
73B GLU* 3.4 28.3 - - + -
74B SER 3.9 6.7 - - - -
75B TRP* 3.8 15.5 - - + -
78B PHE* 3.7 31.2 - + + -
115B ASN 2.9 19.9 + - - +
116B GLN 3.6 2.0 - - - +
118B ALA* 1.3 78.2 - - - +
120B LEU* 1.3 69.8 + - + +
122B GLN* 3.2 13.6 + - - +
123B GLN* 2.9 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TRP* 3.9 26.7 - - + -
78B PHE* 4.2 11.4 - - + -
79B LEU* 4.5 12.3 - - + -
116B GLN 2.9 18.9 + - - +
117B LEU 4.2 0.4 - - - +
119B PHE* 1.3 84.6 - - + +
121B THR* 1.3 60.9 + - - +
123B GLN* 3.2 9.0 + - - +
124B GLY 3.2 1.0 + - - -
125B PHE* 3.1 40.5 + - + -
130B ALA* 3.7 29.8 - - + +
133B ALA* 5.0 4.3 - - + -
134B LEU* 3.8 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 4.5 8.3 - - + +
117B LEU 2.8 25.1 + - - +
118B ALA* 3.1 14.6 + - - -
120B LEU* 1.3 76.2 - - - +
122B GLN* 1.3 60.4 + - - +
124B GLY* 3.1 13.5 + - - -
125B PHE 3.3 21.4 - - - +
126B SER 4.1 1.8 - - - +
127B LEU* 3.9 34.8 - - + +
130B ALA* 4.4 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ALA* 2.9 34.9 + - - +
119B PHE* 3.2 13.9 + - - +
121B THR* 1.3 75.7 - - - +
123B GLN* 1.3 71.6 + - - +
124B GLY 3.2 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU 5.2 2.9 - - - -
74B SER* 5.5 1.9 - - - -
75B TRP* 3.9 40.0 + - + +
119B PHE* 2.9 53.2 + - + +
120B LEU 3.2 7.4 + - - +
121B THR 3.2 0.6 - - - -
122B GLN* 1.3 90.2 + - - +
124B GLY* 1.3 55.7 + - - +
125B PHE* 3.7 1.3 + - + -
201B LEU* 4.1 8.0 - - - +
----------------------------------------------------------
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