Contacts of the helix formed by residues 107 - 122 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A CYS 4.6 3.3 + - - +
61A PHE* 4.8 0.4 - - - -
93A PHE 4.9 1.1 - - - +
94A PHE* 3.3 15.7 - - - +
95A VAL* 2.7 52.6 + - + +
104A TYR* 3.2 20.1 + - + +
106A ARG* 1.3 76.5 - - - +
108A PRO* 1.4 71.8 - - - +
109A ARG* 3.0 19.2 + - - +
110A ASN* 2.9 30.5 + - + +
111A ILE* 3.2 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A CYS* 3.4 19.3 - - + +
27A ASP 3.4 13.9 - - - +
28A LEU* 4.2 7.9 - - + -
61A PHE* 4.5 1.6 - - + -
106A ARG 3.2 10.7 - - - +
107A ASP* 1.4 89.2 - - - +
109A ARG* 1.3 60.7 + - - +
111A ILE* 3.1 13.5 + - - +
112A ALA 3.2 9.5 + - - -
375A ASN* 3.2 40.6 - - - +
377A TYR* 3.3 21.6 - - + +
378A LEU* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 5.2 0.4 - - - +
26A CYS* 4.5 12.6 - - + +
32A MET* 5.1 2.5 - - - -
74A ASP* 2.8 27.5 + - - +
77A THR* 3.7 5.7 - - - +
92A ASN* 4.0 14.7 - - - +
93A PHE 3.3 30.0 + - - +
94A PHE* 3.4 42.4 - - + -
107A ASP* 3.0 11.9 + - - +
108A PRO* 1.3 76.5 - - - +
110A ASN* 1.3 61.4 + - - +
112A ALA* 3.5 4.3 + - - +
113A ARG* 3.1 21.0 + - - +
236A LEU* 4.1 8.7 - - + +
240A ASP* 2.9 37.4 + - - -
377A TYR* 3.6 34.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 4.5 0.9 - - - -
103A PRO* 3.4 25.4 + - + +
104A TYR 3.1 24.6 + - - +
105A SER* 4.5 1.4 - - - +
107A ASP* 2.9 25.3 + - + +
109A ARG* 1.3 75.7 - - - +
111A ILE* 1.3 59.7 + - - +
113A ARG* 3.1 35.5 + - - +
114A LYS* 2.9 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER 3.5 18.4 - - - +
106A ARG 5.4 0.4 - - - -
107A ASP 3.4 14.8 - - - +
108A PRO* 3.1 6.4 + - + +
110A ASN* 1.3 75.9 - - - +
112A ALA* 1.3 59.1 + - - +
114A LYS* 3.3 17.5 + - - +
115A ALA* 2.8 27.9 + - - +
377A TYR 5.2 0.2 - - - +
378A LEU* 3.7 22.7 - - + -
381A SER* 3.8 9.4 - - - +
442A VAL* 3.5 23.4 - - + +
443A PHE* 3.9 30.1 - - + -
447A LEU* 3.4 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO 3.2 7.7 + - - +
109A ARG 3.6 8.7 - - - +
111A ILE* 1.3 76.0 - - - +
113A ARG* 1.3 65.1 + - - +
115A ALA* 3.2 3.8 + - - +
116A GLU* 3.0 28.0 + - - +
235A LEU* 3.8 19.0 - - + +
236A LEU* 3.7 22.9 - - + -
377A TYR* 4.1 13.7 + - + +
381A SER* 3.4 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 3.2 66.1 - - + +
95A VAL 5.3 0.2 + - - -
96A HIS* 3.9 8.3 + - - -
103A PRO* 3.7 22.5 - - - +
107A ASP* 5.1 0.2 + - - -
109A ARG 3.1 11.2 + - - +
110A ASN* 3.1 31.9 + - - +
112A ALA* 1.3 74.0 - - - +
114A LYS* 1.3 64.3 + - - +
116A GLU* 3.2 9.7 + - - +
117A ASN* 3.2 35.3 + - - +
236A LEU* 4.6 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER* 4.6 5.5 + - - +
110A ASN* 2.9 42.5 + - - +
111A ILE* 3.6 20.8 - - - +
112A ALA 3.3 0.2 - - - -
113A ARG* 1.3 77.3 - - + +
115A ALA* 1.3 57.8 + - - +
117A ASN* 3.4 8.3 + - - +
118A TYR* 2.9 30.7 + - - +
440A GLY 5.6 2.0 - - - +
441A GLY 3.0 20.5 + - - +
442A VAL* 2.8 36.0 + - + +
444A THR* 4.1 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE 2.8 14.9 + - - +
112A ALA 3.2 9.4 + - - +
114A LYS* 1.3 77.2 - - - +
116A GLU* 1.3 62.0 + - - +
118A TYR* 3.2 4.6 + - - +
119A LEU* 3.0 23.2 + - - +
235A LEU* 4.2 13.5 - - + -
381A SER* 3.5 25.1 - - - +
384A LEU* 4.0 12.1 - - + +
385A MET* 5.1 2.6 - - - +
442A VAL* 3.9 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA 3.0 15.0 + - - +
113A ARG* 3.8 8.2 - - - +
115A ALA* 1.3 73.9 - - - +
117A ASN* 1.3 63.2 - - - +
119A LEU* 3.5 12.0 - - + +
120A ILE* 3.3 28.4 + - + +
126A ASP 5.0 1.0 - - - +
128A ALA* 6.3 2.0 - - + +
234A SER* 3.6 14.0 + - - -
235A LEU* 3.2 27.1 + - + -
236A LEU* 3.0 44.4 + - - +
237A HIS* 4.7 0.5 + - - -
384A LEU* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 3.2 27.0 + - - +
114A LYS* 3.7 10.0 - - - +
116A GLU* 1.3 77.3 - - - +
118A TYR* 1.3 65.2 + - - +
120A ILE* 3.1 18.3 + - - +
121A SER* 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS 2.9 18.8 + - - +
115A ALA 3.2 4.0 + - - +
117A ASN* 1.3 74.3 - - - +
119A LEU* 1.3 66.7 + - - +
121A SER* 2.7 31.0 + - - -
122A THR* 3.0 27.2 + - + +
385A MET* 3.7 27.8 - - + -
388A LEU* 4.0 19.7 - - + -
392A LYS* 3.3 21.2 + - - +
439A GLU* 3.6 26.4 + - + +
440A GLY* 3.8 31.6 - - - +
442A VAL* 3.6 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA 3.0 12.4 + - - +
116A GLU* 3.5 13.0 - - + +
118A TYR* 1.3 77.2 - - - +
120A ILE* 1.3 61.9 + - - +
122A THR* 2.7 25.4 + - - +
123A GLY 3.7 0.5 + - - -
125A ALA* 3.2 37.2 - - + +
126A ASP 4.0 3.4 - - - +
127A THR* 3.5 16.8 - - - +
128A ALA* 3.4 40.6 - - + +
281A LEU* 4.2 5.2 - - + -
384A LEU* 4.2 9.6 - - + -
388A LEU* 3.8 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 3.3 17.7 + - + +
117A ASN* 3.1 21.1 + - - +
119A LEU* 1.3 75.7 - - - +
121A SER* 1.3 64.7 + - - +
123A GLY* 3.1 15.1 + - - -
125A ALA 3.8 6.8 - - - +
126A ASP* 3.7 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN 3.0 12.7 + - - -
118A TYR* 2.7 34.6 + - - -
120A ILE* 1.3 79.0 - - - +
122A THR* 1.3 59.4 + - - +
123A GLY 3.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 3.0 42.2 + - + +
119A LEU* 2.7 21.6 + - - +
120A ILE 3.1 0.2 + - - -
121A SER* 1.3 77.4 - - - +
123A GLY* 1.3 55.9 + - - +
124A ILE* 3.1 36.5 + - + +
388A LEU* 4.7 3.4 - - + -
392A LYS* 3.2 31.8 - - - +
----------------------------------------------------------
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