Contacts of the helix formed by residues 89 - 104 (chain A) in PDB entry 1EZF
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 SER 89 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR 4.0 2.2 + - - -
88A ILE* 1.3 75.2 - - - +
90A VAL* 1.3 65.0 + - - +
91A GLU* 3.2 23.2 + - - +
92A LYS* 3.0 28.6 + - - +
93A LYS* 3.0 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE 3.9 0.6 + - - +
89A SER* 1.3 72.6 - - - +
91A GLU* 1.3 83.5 + - + +
93A LYS* 4.3 2.0 - - + +
94A VAL* 3.0 40.6 + - + +
158A LEU* 4.0 37.9 - - + +
159A ASP* 4.6 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 3.1 23.8 - - - +
90A VAL* 1.3 97.9 + - + +
92A LYS* 1.3 60.6 + - + +
94A VAL* 4.8 1.1 - - - +
95A PRO* 3.4 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.6 28.4 - - + +
89A SER* 3.0 17.3 + - - +
91A GLU* 1.3 78.9 - - + +
93A LYS* 1.3 63.6 + - - +
95A PRO* 3.2 12.4 - - - +
96A LEU* 3.5 20.1 + - + +
111A PHE* 4.4 10.3 - - - -
113A GLU* 4.2 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.1 23.8 - - + +
83A GLU* 2.7 28.8 + - - +
85A ASP 2.8 20.1 + - - -
86A MET* 3.4 18.6 - - - +
88A ILE* 3.4 34.8 - - + +
89A SER 3.0 14.1 + - - +
90A VAL* 3.4 1.8 + - + +
92A LYS* 1.3 74.6 - - - +
94A VAL* 1.3 57.7 + - - +
96A LEU* 2.9 10.2 + - + +
97A LEU* 2.7 43.0 + - + +
158A LEU* 3.7 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 3.0 24.1 + - + +
91A GLU* 4.8 1.3 - - - +
93A LYS* 1.3 73.1 - - - +
95A PRO* 1.3 68.2 - - + +
97A LEU* 3.8 2.6 - - - +
98A HIS* 2.9 62.9 + - + +
155A ALA* 4.3 16.6 - - + +
158A LEU* 4.3 13.5 - - + -
159A ASP* 6.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU 3.4 14.8 - - - +
92A LYS* 3.2 14.6 - - - +
94A VAL* 1.3 96.2 - - + +
96A LEU* 1.3 55.9 + - + +
98A HIS* 4.3 5.8 - - + +
99A ASN* 2.8 44.9 + - - +
103A PHE* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.5 20.3 - - + +
88A ILE* 4.9 6.3 - - + -
92A LYS* 3.5 23.1 + - + +
93A LYS* 2.9 12.0 + - + +
95A PRO* 1.3 77.6 - - + +
97A LEU* 1.3 65.4 + - + +
100A PHE* 3.1 25.6 + - - +
103A PHE* 3.6 30.1 - - + -
109A TRP* 4.0 17.3 - - + +
111A PHE* 3.3 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.0 10.5 - - + +
82A LEU* 4.3 8.5 - - + -
83A GLU* 4.1 19.1 - - + +
93A LYS* 2.7 27.6 + - + +
94A VAL 3.8 2.7 - - - +
96A LEU* 1.3 74.3 - - + +
98A HIS* 1.3 62.5 + - - +
100A PHE* 3.6 11.4 + - - +
101A HIS 5.2 0.2 + - - -
147A CYS 4.7 0.3 - - - +
151A GLY* 3.1 31.8 - - - +
154A MET* 3.5 35.7 - - + -
155A ALA* 3.5 31.6 - - + +
158A LEU* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 2.9 44.4 + - + +
95A PRO* 3.9 6.1 - - + +
97A LEU* 1.3 79.7 - - - +
99A ASN* 1.3 61.2 + - - +
101A HIS* 3.1 24.6 + - - -
148A ARG* 5.2 5.2 - - - +
151A GLY 4.6 1.8 - - - -
152A ILE* 3.6 47.7 + - + +
155A ALA* 3.3 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 2.8 33.3 + - - +
96A LEU 3.8 0.9 - - - -
98A HIS* 1.3 76.7 - - - +
100A PHE* 1.3 64.8 + - - +
101A HIS* 3.3 9.7 - - - -
102A SER* 3.0 25.3 + - - -
103A PHE* 3.1 33.5 + - + -
106A GLN* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.2 46.2 - - + -
78A ALA* 3.9 9.0 - - + -
79A LEU* 3.7 46.0 - - + -
82A LEU* 4.3 11.4 - - + -
96A LEU 3.1 13.1 + - - +
97A LEU 3.7 11.0 - - - +
98A HIS 3.4 2.2 - - - -
99A ASN* 1.3 76.1 - - - +
101A HIS* 1.3 65.3 + - - +
103A PHE* 2.8 36.6 + + - +
104A LEU* 3.3 14.3 - - + +
109A TRP* 4.8 5.4 - + - -
125A PHE* 3.8 28.9 - + - -
147A CYS* 3.9 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU 5.2 0.2 + - - -
98A HIS 3.1 26.4 + - - -
99A ASN* 3.8 7.6 - - - -
100A PHE* 1.3 78.3 - - - +
102A SER* 1.3 84.7 + - - +
104A LEU* 3.2 33.2 - - + +
105A TYR* 3.9 8.3 - - - -
144A ALA* 3.8 15.7 - - + +
147A CYS* 4.1 5.3 + - + +
148A ARG* 3.6 58.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASN* 3.0 18.8 + - - -
101A HIS* 1.3 100.6 + - - +
103A PHE* 1.3 57.7 + - - +
105A TYR* 2.9 27.1 + - - +
106A GLN* 3.4 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 5.7 0.4 - - + -
95A PRO 4.6 1.1 - - - -
96A LEU* 3.6 34.8 - - + -
99A ASN* 3.1 28.4 + - + -
100A PHE* 2.8 27.4 + + + +
102A SER* 1.3 73.4 - - - +
104A LEU* 1.3 63.3 + - - +
105A TYR 3.1 0.2 - - - -
106A GLN* 3.1 48.3 + - - +
109A TRP* 3.4 63.4 - + + +
125A PHE* 3.7 13.9 - - + -
129A SER* 4.4 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 4.4 6.7 - - + -
100A PHE* 3.3 31.6 - - + +
101A HIS* 3.2 17.9 - - - +
103A PHE* 1.3 76.7 - - - +
105A TYR* 1.3 60.9 - - + +
125A PHE* 3.8 27.1 - - + -
129A SER* 3.5 7.8 - - - -
132A PHE* 3.6 44.3 - - + -
133A ARG* 2.9 28.9 + - - +
143A ILE* 4.7 2.0 - - + -
144A ALA* 4.0 22.4 - - + +
147A CYS* 4.6 8.5 - - - -
----------------------------------------------------------
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