Contacts of the helix formed by residues 107 - 122 (chain B) in PDB entry 3ZXR
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 107 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B CYS 4.5 3.6 + - - +
61B PHE* 4.8 1.8 - - - -
93B PHE 5.0 1.1 - - - +
94B PHE* 3.3 15.8 - - - +
95B VAL* 2.7 51.2 + - + +
104B TYR* 3.2 19.4 + - + +
106B ARG* 1.3 76.9 - - - +
108B PRO* 1.4 74.8 - - - +
109B ARG* 3.0 16.9 + - - +
110B ASN* 3.0 29.5 + - + +
111B ILE* 3.1 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B CYS* 3.3 20.4 - - + +
27B ASP 3.3 15.0 - - - +
28B LEU* 4.2 8.7 - - + -
61B PHE* 4.5 2.0 - - + -
106B ARG 3.3 9.8 - - - +
107B ASP* 1.4 90.0 - - - +
109B ARG* 1.3 60.9 + - - +
111B ILE* 3.1 12.5 + - - +
112B ALA 3.2 9.5 + - - -
375B ASN* 3.3 32.5 - - - +
377B TYR* 3.3 27.5 - - + +
378B LEU* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 5.2 0.4 - - - +
26B CYS* 4.5 13.7 - - + +
32B MET* 5.1 1.8 - - - -
74B ASP* 2.8 27.5 + - - +
77B THR* 3.7 4.8 - - - +
92B ASN* 4.0 13.8 - - - +
93B PHE 3.3 30.1 + - - +
94B PHE* 3.5 43.7 - - + -
107B ASP* 3.0 12.8 + - - +
108B PRO* 1.3 75.6 - - - +
110B ASN* 1.3 62.1 + - - +
112B ALA* 3.5 3.3 + - - +
113B ARG* 3.1 21.0 + - - +
236B LEU* 4.1 9.2 - - + +
240B ASP* 2.8 36.9 + - - -
377B TYR* 3.6 34.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PHE* 4.2 0.4 - - - -
95B VAL 5.5 0.2 - - - +
103B PRO* 3.4 27.1 + - + +
104B TYR 3.0 25.7 + - - +
105B SER* 4.5 1.2 - - - +
107B ASP* 3.0 22.3 + - + +
109B ARG* 1.3 75.6 - - - +
111B ILE* 1.3 61.4 + - - +
113B ARG* 3.1 33.6 + - - +
114B LYS* 2.8 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 6.3 0.2 - - + -
105B SER 3.5 18.2 - - - +
106B ARG 5.4 0.4 - - - -
107B ASP 3.1 14.5 + - - +
108B PRO* 3.1 6.9 + - + +
110B ASN* 1.3 75.7 - - - +
112B ALA* 1.3 57.0 + - - +
114B LYS* 3.3 16.2 + - - +
115B ALA* 2.8 28.1 + - - +
377B TYR 5.3 0.2 - - - +
378B LEU* 3.7 16.4 - - + -
381B SER* 4.0 9.6 - - - +
442B VAL* 3.5 26.5 - - + +
443B PHE* 3.9 30.7 - - + -
447B LEU* 3.5 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PRO 3.2 8.9 + - - +
109B ARG 3.7 8.3 - - - +
110B ASN 3.3 0.2 - - - -
111B ILE* 1.3 77.6 - - - +
113B ARG* 1.3 62.7 + - - +
115B ALA* 3.2 3.1 + - - +
116B GLU* 3.1 29.1 + - - +
235B LEU* 3.7 20.2 - - + +
236B LEU* 3.7 20.9 - - + -
377B TYR* 4.2 13.5 - - + +
381B SER* 3.4 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PHE* 3.2 64.7 - - + +
95B VAL 5.3 0.4 + - - -
96B HIS* 4.0 7.9 + - - -
103B PRO* 3.8 22.1 - - - +
107B ASP* 5.1 0.2 + - - -
109B ARG 3.1 11.8 + - - +
110B ASN* 3.1 31.8 + - - +
112B ALA* 1.3 76.1 - - - +
114B LYS* 1.3 64.2 + - + +
116B GLU* 3.3 9.0 + - - +
117B ASN* 3.2 36.4 + - - +
236B LEU* 4.6 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 4.7 5.9 + - - +
110B ASN* 2.8 46.3 + - - +
111B ILE* 3.6 21.3 - - - +
113B ARG* 1.3 74.4 - - + +
115B ALA* 1.3 57.3 + - - +
117B ASN* 3.2 9.2 + - - +
118B TYR* 2.8 30.8 + - - +
440B GLY 5.6 1.6 - - - +
441B GLY 2.9 20.4 + - - +
442B VAL* 2.7 37.0 + - + +
444B THR* 4.0 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE 2.8 17.3 + - - +
112B ALA 3.2 6.3 + - - +
114B LYS* 1.3 76.3 - - - +
116B GLU* 1.3 62.5 + - - +
118B TYR* 3.3 2.8 + - - +
119B LEU* 3.0 23.9 + - - +
235B LEU* 4.2 12.1 - - + -
381B SER* 3.6 23.1 - - - +
384B LEU* 3.9 11.0 - - + +
385B MET* 5.1 2.2 - - - -
442B VAL* 3.9 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA 3.1 13.2 + - - +
113B ARG* 3.3 8.0 + - - +
115B ALA* 1.3 75.5 - - - +
117B ASN* 1.3 64.0 + - - +
119B LEU* 3.4 11.1 + - + +
120B ILE* 3.3 29.2 + - + +
126B ASP 5.0 1.7 - - - +
128B ALA* 6.0 1.5 + - + +
234B SER* 3.6 14.0 + - - -
235B LEU* 3.3 27.2 + - + -
236B LEU* 3.1 42.9 + - - +
237B HIS* 5.9 0.2 - - - -
384B LEU* 5.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ARG* 3.2 26.5 + - - +
114B LYS* 3.7 10.3 - - - +
116B GLU* 1.3 75.9 - - - +
118B TYR* 1.3 64.0 + - - +
120B ILE* 3.1 18.6 + - - +
121B SER* 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LYS 2.8 16.3 + - - +
115B ALA 3.7 2.7 - - - +
117B ASN* 1.3 72.7 - - - +
119B LEU* 1.3 69.5 + - - +
121B SER* 2.8 30.1 + - - -
122B THR* 3.1 26.9 + - + +
385B MET* 3.6 30.3 - - + -
388B LEU* 4.0 17.9 - - + -
392B LYS* 3.3 20.1 + - - +
439B GLU* 3.5 26.0 + - + +
440B GLY* 3.7 32.5 - - - +
442B VAL* 3.6 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ALA 3.0 12.7 + - - +
116B GLU* 3.5 12.3 - - + +
118B TYR* 1.3 77.2 - - - +
120B ILE* 1.3 61.1 + - - +
122B THR* 2.7 26.7 + - - +
123B GLY 3.7 0.2 + - - -
125B ALA* 3.2 34.7 - - + +
126B ASP 4.0 2.9 - - - +
127B THR* 3.6 16.6 - - - +
128B ALA* 3.5 40.8 - - + +
281B LEU* 4.3 5.8 - - + -
384B LEU* 4.2 9.2 - - + -
388B LEU* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 3.3 17.2 + - + +
117B ASN* 3.1 20.7 + - - +
119B LEU* 1.3 75.3 - - - +
121B SER* 1.3 64.4 + - - +
123B GLY* 3.1 16.5 + - - -
125B ALA 3.8 7.5 - - - +
126B ASP* 3.7 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASN 3.0 12.7 + - - -
118B TYR* 2.8 31.3 + - - -
120B ILE* 1.3 79.1 - - - +
122B THR* 1.3 58.6 + - - +
123B GLY 3.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR* 3.1 37.4 + - + +
119B LEU* 2.7 21.9 + - - +
121B SER* 1.3 77.6 - - - +
123B GLY* 1.3 56.7 + - - +
124B ILE* 3.1 35.8 + - + +
388B LEU* 4.7 3.4 - - + -
392B LYS* 3.3 32.3 + - - +
----------------------------------------------------------
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