Contacts of the helix formed by residues 101 - 115 (chain D) in PDB entry 2ZXI
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 101 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D THR 3.1 19.8 + - - +
80D ILE* 3.9 13.6 - - + +
100D ALA* 1.3 71.8 - - - +
102D LYS* 1.3 63.2 + - - +
103D LYS* 3.3 13.5 + - - +
104D ARG* 3.0 44.9 + - + +
105D TYR* 2.9 20.8 + - - +
307D GLU 3.7 4.5 - - - -
308D GLY* 3.6 11.9 - - - -
309D LEU* 2.9 28.9 + - - +
310D ASP* 4.6 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D MET* 3.3 52.1 + - + +
47D SER* 4.0 0.6 - - - +
48D CYS 2.9 27.5 + - - -
50D PRO* 3.7 22.9 - - + -
100D ALA 3.2 4.2 + - - -
101D ASP* 1.3 71.4 - - - +
103D LYS* 1.3 62.5 + - - +
105D TYR* 3.3 2.5 + - - +
106D ARG* 3.0 32.3 + - - +
205D ARG* 3.5 14.8 - - - +
307D GLU* 2.9 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ARG* 5.1 0.4 - - - +
107C GLU* 3.0 44.6 - - + +
111C LYS* 6.3 0.2 - - - +
101D ASP* 3.2 10.0 + - - +
102D LYS* 1.3 81.2 - - - +
104D ARG* 1.3 73.2 + - + +
106D ARG* 3.3 27.6 + - - +
107D GLU* 3.0 45.5 + - + +
307D GLU 4.6 1.2 + - - +
310D ASP* 3.1 34.4 + - - +
311D THR* 6.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D GLN* 5.8 1.6 - - - +
78D THR* 3.4 19.6 - - + +
80D ILE* 5.6 0.8 - - - +
101D ASP* 3.0 36.5 + - - +
103D LYS* 1.3 85.8 - - + +
105D TYR* 1.3 57.0 + - - +
107D GLU* 3.8 11.6 - - - +
108D TYR* 2.9 30.7 + - - +
309D LEU* 3.4 30.8 - - - +
310D ASP* 3.8 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D HIS* 4.4 9.3 - + - -
44D GLY* 3.6 18.6 - - - -
46D MET* 3.9 28.3 - - + -
52D ILE* 4.1 20.2 - - + -
71D MET* 3.4 32.7 - - - +
74D ALA* 3.7 17.0 - - + -
75D ILE* 4.1 9.9 - - + -
78D THR* 3.5 26.4 - - - +
100D ALA* 4.5 6.7 - - + -
101D ASP 2.9 12.6 + - - +
102D LYS 3.5 8.5 - - - +
104D ARG* 1.3 75.1 - - - +
106D ARG* 1.3 65.7 + - - +
108D TYR* 3.3 3.6 + - - +
109D MET* 3.1 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASP* 4.1 27.7 + - - +
106C ARG* 4.4 17.9 - - - +
107C GLU* 5.4 0.4 + - - -
41D ASP 3.7 22.0 - - - +
42D THR* 4.9 2.0 - - - +
43D ILE 3.3 23.6 - - - +
44D GLY 3.8 16.4 - - - +
45D GLN* 4.1 26.8 + - + +
102D LYS* 3.0 17.0 + - - +
103D LYS* 3.6 43.2 + - - +
105D TYR* 1.3 76.3 - - - +
107D GLU* 1.3 68.7 + - - +
109D MET* 3.1 3.6 + - - -
110D LYS* 2.9 21.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS* 2.7 38.7 + - + +
104C ARG* 2.8 17.0 + - - -
106C ARG* 6.2 0.7 - - - +
107C GLU* 2.5 31.5 - - - +
103D LYS* 3.0 29.4 + - + +
104D ARG* 3.8 11.9 - - - +
106D ARG* 1.3 86.3 - - - +
108D TYR* 1.3 63.8 + - - +
110D LYS* 3.2 7.1 + - - +
111D LYS* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D GLU* 3.0 28.0 + - - -
73D LYS* 3.5 18.2 - - - +
74D ALA* 3.5 34.3 - - + -
77D GLN* 4.1 38.4 - - + -
78D THR* 3.9 7.4 - - + -
104D ARG 2.9 20.1 + - - +
105D TYR* 3.5 4.7 - - - +
106D ARG 3.2 0.2 - - - -
107D GLU* 1.3 77.2 - - - +
109D MET* 1.3 65.4 + - - +
111D LYS* 3.3 6.2 + - - +
112D VAL* 3.0 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D HIS* 6.1 1.1 - - + -
20D ILE* 3.8 37.2 - - + -
21D GLU* 4.1 7.0 - - - +
24D LEU* 5.3 0.9 - - - -
43D ILE* 4.8 1.1 - - - -
44D GLY* 4.1 5.6 - - - -
70D GLU* 4.1 13.9 - - + -
71D MET* 3.9 20.4 - - + +
74D ALA* 3.8 11.4 - - + -
105D TYR* 3.1 49.1 + - + +
106D ARG 3.7 7.2 - - - +
108D TYR* 1.3 91.8 - - + +
110D LYS* 1.3 64.5 + - - +
112D VAL* 4.2 2.8 - - - +
113D CYS* 3.1 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C THR* 5.2 0.8 + - - -
313C GLU* 4.2 14.6 + - - -
345C ARG* 4.5 0.4 - - - +
40D ALA* 3.3 31.3 + - - +
41D ASP* 4.2 12.6 + - - +
43D ILE* 3.9 27.3 + - + +
106D ARG* 2.9 14.5 + - + +
107D GLU* 3.6 11.2 - - - +
109D MET* 1.3 73.6 - - - +
111D LYS* 1.3 60.4 + - - +
113D CYS* 3.4 1.0 + - - +
114D GLU* 2.9 73.4 + - + +
121D ILE* 4.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ASP* 3.5 42.6 + - + +
107D GLU 2.9 17.0 + - - +
108D TYR* 3.7 6.7 - - - +
110D LYS* 1.3 75.8 - - - +
112D VAL* 1.3 67.5 + - + +
114D GLU* 3.9 4.9 - - - +
115D ASN* 2.9 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D LEU* 4.2 6.1 - - + -
28D ARG* 3.3 30.5 - - - +
70D GLU* 3.9 15.5 - - + +
108D TYR* 3.0 47.7 + - + +
109D MET* 4.2 5.2 - - - +
111D LYS* 1.3 77.1 - - + +
113D CYS* 1.3 63.4 + - - +
115D ASN* 3.9 2.1 - - - +
116D GLN* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE* 3.8 35.4 - - - -
24D LEU* 4.1 15.0 - - - -
35D MET* 4.1 13.9 - - - -
43D ILE* 4.6 5.6 - - + -
109D MET 3.1 25.7 + - - +
110D LYS* 3.8 4.5 - - - +
112D VAL* 1.3 77.8 - - - +
114D GLU* 1.3 62.7 + - - +
116D GLN* 3.2 16.6 + - - +
119D LEU* 3.5 24.1 - - + +
121D ILE* 4.5 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ARG* 3.7 11.1 + - - -
310C ASP* 4.6 2.1 - - - +
311C THR* 2.5 39.4 + - - -
312C ILE* 2.8 48.9 + - + +
313C GLU* 4.1 4.0 + - - +
110D LYS* 2.9 64.6 + - - +
111D LYS* 3.9 4.1 + - - +
113D CYS* 1.3 74.2 - - - +
115D ASN* 1.3 67.1 + - - +
116D GLN 3.3 0.7 + - - -
119D LEU 4.7 1.1 - - - +
121D ILE* 3.8 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ARG* 4.5 5.0 + - - +
310C ASP 3.3 22.2 + - - +
312C ILE* 3.4 23.0 - - - +
111D LYS* 2.9 40.4 + - - +
112D VAL* 3.9 2.7 - - - +
114D GLU* 1.3 76.5 - - - +
116D GLN* 1.3 63.2 + - - +
117D GLU* 3.4 3.6 + - - +
----------------------------------------------------------
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