Contacts of the helix formed by residues 111 - 123 (chain A) in PDB entry 1Z59
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 GLY 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 3.4 29.9 - - - +
108A TYR* 3.3 15.5 + - - +
109A GLY 3.3 3.8 - - - -
110A LEU* 1.3 75.6 - - - +
112A VAL* 1.3 63.9 + - - -
113A LYS 3.1 1.2 + - - -
114A ALA* 3.1 16.6 + - - +
115A ALA 4.2 0.3 + - - -
1001A MG 4.4 2.2 - - - -
2001A ADP 3.8 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 3.7 17.7 + - + -
39A LEU* 3.6 30.7 - - + -
42A ASN* 3.5 19.7 - - - +
89A ALA 4.4 4.5 - - - +
90A PHE* 3.8 31.2 - - + -
111A GLY* 1.3 70.6 - - - -
113A LYS* 1.3 66.6 + - - +
114A ALA 3.1 0.2 - - - -
115A ALA* 3.0 15.3 + - + +
116A VAL* 3.1 11.6 + - + +
174A ILE* 4.1 13.0 - - + -
2001A ADP 3.1 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN 3.5 6.9 + - - -
89A ALA* 3.1 29.1 + - - +
90A PHE* 3.8 16.6 - - - +
91A GLY* 5.2 0.2 - - - -
92A ARG 3.4 35.9 + - - +
93A VAL* 4.0 21.7 - - + +
94A LEU* 5.0 13.6 - - - +
110A LEU* 3.1 16.1 + - + +
111A GLY 3.1 0.8 - - - -
112A VAL* 1.3 78.6 - - - +
114A ALA* 1.3 55.9 + - - +
116A VAL* 3.7 7.6 - - - +
117A LEU* 2.9 31.9 + - - +
146A ILE* 5.3 3.0 - - + +
2001A ADP 3.1 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.7 32.7 - - + -
23A ALA 5.2 1.3 - - - +
25A PHE* 3.7 16.4 - - + -
108A TYR* 6.1 3.1 - - + -
110A LEU* 3.8 22.4 + - + +
111A GLY 3.1 13.9 + - - +
113A LYS* 1.3 78.3 - - - +
115A ALA* 1.3 56.7 + - - +
117A LEU* 4.4 1.3 - - - -
118A TYR* 2.9 30.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
25A PHE* 3.8 16.5 - - + -
35A THR* 3.5 39.3 - - + +
38A GLU* 5.3 2.9 - - + -
111A GLY 4.2 0.8 + - - -
112A VAL* 3.0 15.8 + - + +
114A ALA* 1.3 77.0 - - - +
116A VAL* 1.3 56.8 + - - +
118A TYR* 3.5 1.4 + - - +
119A SER* 2.9 30.3 + - - -
174A ILE* 3.9 14.9 - - + +
176A ILE* 4.1 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.5 34.1 - - + +
112A VAL 3.1 15.4 + - - +
113A LYS* 3.7 8.3 - - - +
114A ALA 3.3 0.2 - - - -
115A ALA* 1.3 75.3 - - - +
117A LEU* 1.3 57.5 + - - +
119A SER* 3.3 8.7 + - - -
120A GLN* 3.0 46.6 + - - +
127A ILE* 3.8 31.0 - - + -
144A LEU* 4.9 0.9 - - + -
146A ILE* 3.7 15.5 - - + +
174A ILE* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA* 3.9 26.5 - - + +
16A PHE* 3.6 28.3 - - + -
17A LYS* 4.1 16.8 - - + -
93A VAL* 4.8 5.2 - - + -
110A LEU* 4.2 14.1 - - + -
113A LYS 2.9 19.1 + - - +
114A ALA 3.8 4.0 - - - +
116A VAL* 1.3 73.7 - - - +
118A TYR* 1.3 62.8 + - - +
120A GLN* 3.3 1.6 + - - +
121A MSE 3.0 32.8 + - + +
146A ILE* 3.9 19.6 - - + +
148A ILE* 3.9 27.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
16A PHE* 4.4 3.7 - + + -
20A PRO* 5.6 2.5 - - + -
25A PHE* 3.8 36.6 - + + -
27A ASN* 4.1 2.4 - - - -
28A PRO* 3.7 24.8 - - - +
31A ALA* 3.3 32.3 - - + +
114A ALA 2.9 22.1 + - - +
115A ALA 3.7 3.6 - - - +
117A LEU* 1.3 71.7 - - - +
119A SER* 1.3 62.7 + - - +
121A MSE 3.2 24.3 + - + -
122A HIS* 3.3 47.5 + + - +
176A ILE* 3.8 17.3 - - + -
177A PRO* 3.8 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA 2.9 14.8 + - - -
116A VAL* 3.3 10.3 - - - -
118A TYR* 1.3 78.1 - - - +
120A GLN* 1.3 68.0 + - - +
123A GLN* 3.0 43.4 + - - +
125A LYS 4.0 2.4 + - - -
127A ILE* 4.6 3.3 - - - +
174A ILE* 3.8 15.1 - - - +
175A SER 2.7 30.4 + - - -
176A ILE* 3.9 5.8 - - - +
177A PRO* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 3.0 35.3 + - - +
117A LEU 3.3 1.1 + - - +
119A SER* 1.3 76.9 + - - +
121A MSE 1.3 63.7 + - - +
122A HIS 3.5 0.3 + - - -
123A GLN* 3.8 11.3 + - - +
125A LYS 3.3 22.7 - - - +
126A PRO* 4.3 1.6 - - - +
127A ILE* 4.3 7.1 + - - +
145A LYS* 3.3 35.2 - - + +
146A ILE* 3.3 36.6 - - + +
148A ILE* 3.7 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 4.3 11.2 - - + -
17A LYS* 4.0 37.2 - - + +
20A PRO* 5.6 7.4 - - + -
117A LEU* 3.0 35.0 + - + +
118A TYR* 3.2 22.6 + - + +
120A GLN* 1.3 79.3 - - - +
122A HIS* 1.3 102.3 + - + +
148A ILE* 4.5 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.9 2.9 - - - +
118A TYR* 3.3 54.6 + + - +
120A GLN 3.3 0.2 - - - -
121A MSE 1.3 109.3 + - + +
123A GLN* 1.3 63.2 + - - +
177A PRO* 3.5 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.2 22.9 - - + +
119A SER* 3.0 46.8 + - - +
120A GLN* 3.8 13.6 + - - +
121A MSE 3.8 0.4 - - - -
122A HIS* 1.3 79.9 - - - +
124A ASP* 1.3 67.2 + - - +
125A LYS* 2.9 45.8 + - - +
145A LYS* 5.5 0.5 + - - -
175A SER* 3.4 29.0 - - - +
177A PRO* 4.5 9.2 - - + -
----------------------------------------------------------
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