Contacts of the helix formed by residues 90 - 104 (chain A) in PDB entry 4IX8
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 PRO 90 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS 3.6 5.4 - - - +
89A THR* 1.3 95.2 - - + +
91A ASP* 1.3 65.3 + - - +
92A ILE* 3.9 20.0 - - + -
93A VAL* 3.0 18.5 + - + +
94A THR* 3.2 11.5 + - - -
287A TYR 5.4 1.1 - - - +
288A GLN* 4.1 23.3 - - + +
339A CYS* 4.2 16.4 - - + -
343A CYS* 4.0 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR 3.4 4.9 + - - +
90A PRO* 1.3 71.2 - - - +
92A ILE* 1.3 59.0 + - - +
94A THR* 3.2 12.8 + - - +
95A GLU* 2.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 3.9 17.5 - - + -
91A ASP* 1.3 80.0 - - - +
93A VAL* 1.3 59.3 + - + +
95A GLU* 4.0 4.6 - - - +
96A ALA* 3.1 27.7 + - - +
335A THR* 3.5 12.4 - - + +
338A LYS* 4.0 37.9 - - + +
339A CYS* 4.0 19.3 - - - -
340A PRO* 5.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 4.2 5.8 - - + -
90A PRO* 3.0 16.3 + - + +
92A ILE* 1.3 74.1 - - - +
94A THR* 1.3 66.0 + - - +
96A ALA* 3.3 3.5 + - - +
97A MET* 3.0 23.7 + - + +
288A GLN* 3.6 25.6 - - - +
293A TRP* 3.6 31.2 - - + -
331A ALA* 4.4 2.9 - - + +
332A ILE* 4.9 7.9 - - + -
335A THR* 3.4 27.1 - - - +
339A CYS* 3.8 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 4.1 16.1 + - - +
90A PRO 3.2 10.1 + - - -
91A ASP* 3.5 15.7 + - - +
93A VAL* 1.3 80.2 - - - +
95A GLU* 1.3 65.9 + - + +
97A MET* 3.3 9.3 + - - +
98A VAL* 3.2 21.0 + - - +
293A TRP* 5.0 2.3 - - - -
101B VAL* 3.6 33.3 + - + +
102B ARG* 3.9 23.3 - - + +
107B ASN* 5.2 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP* 2.8 26.5 + - + +
92A ILE* 4.3 4.0 - - - +
94A THR* 1.3 74.7 - - + +
96A ALA* 1.3 60.9 + - - +
98A VAL* 3.2 11.7 + - - +
99A ASP* 2.9 38.7 + - - +
102B ARG* 2.9 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE 3.1 19.6 + - - +
93A VAL 3.6 4.7 - - - +
95A GLU* 1.3 74.3 - - - +
97A MET* 1.3 64.9 + - - +
99A ASP* 3.3 9.7 + - - +
100A VAL* 2.9 28.8 + - - +
331A ALA* 3.9 16.8 - - - +
334A ARG* 4.5 11.9 - - + +
335A THR* 3.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL 3.0 19.1 + - - +
94A THR 3.4 9.0 - - - +
95A GLU 3.2 0.2 - - - -
96A ALA* 1.3 75.8 - - - +
98A VAL* 1.3 58.2 + - - +
100A VAL* 3.3 3.3 + - - +
101A VAL* 2.9 33.6 + - - +
293A TRP* 4.0 27.1 - - + +
327A ILE* 3.8 16.8 - - + +
328A CYS* 3.6 38.4 - - - -
331A ALA* 3.5 24.7 - - + -
97B MET* 5.8 4.9 - - + -
101B VAL* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR 3.4 13.7 - - - +
95A GLU* 3.3 15.0 - - - +
96A ALA 3.2 0.2 - - - -
97A MET* 1.3 73.1 - - - +
99A ASP* 1.3 71.4 + - - +
101A VAL* 3.3 10.4 + - - +
102A ARG* 3.0 58.2 + - - +
98B VAL* 4.0 11.0 - - + -
101B VAL* 3.8 19.0 - - + +
102B ARG* 3.7 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLU* 2.9 30.4 + - - +
96A ALA* 3.7 7.7 - - - +
98A VAL* 1.3 78.9 - - - +
100A VAL* 1.3 62.7 + - - +
102A ARG* 3.4 5.0 + - - +
103A SER* 3.1 24.4 + - - -
334A ARG* 3.9 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 2.9 21.1 + - - +
97A MET* 3.6 4.3 - - - +
99A ASP* 1.3 76.4 - - - +
101A VAL* 1.3 62.9 + - - +
103A SER* 2.6 25.5 + - - -
104A GLY 3.8 1.6 + - - -
105A LYS 4.7 0.3 + - - -
106A PHE* 3.8 27.2 + - + +
107A ASN* 5.3 0.2 - - - +
327A ILE* 3.6 31.1 - - + +
330A GLU* 3.5 26.2 - - + -
331A ALA* 3.9 12.8 - - - +
334A ARG* 3.6 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET 2.9 17.2 + - - +
98A VAL* 3.4 11.4 - - - +
100A VAL* 1.3 76.5 - - - +
102A ARG* 1.3 67.1 + - - +
104A GLY* 3.3 13.0 + - - -
107A ASN* 4.6 4.9 + - - +
327A ILE* 3.9 22.9 - - + -
94B THR* 3.6 20.9 + - + +
97B MET* 4.0 35.4 - - + -
98B VAL* 3.8 24.0 - - + +
101B VAL* 6.4 0.7 - - + -
293B TRP* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 3.0 41.4 + - - +
99A ASP* 4.0 5.2 - - - +
101A VAL* 1.3 78.4 - - - +
103A SER* 1.3 62.9 + - - +
104A GLY* 3.3 1.7 + - - -
94B THR* 3.9 12.2 - - + +
95B GLU* 3.1 39.1 + - - +
98B VAL* 3.6 23.1 - - + +
102B ARG* 3.8 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP 3.1 15.8 + - - -
100A VAL* 2.6 20.1 + - - -
102A ARG* 1.3 78.2 - - - +
104A GLY* 1.3 59.8 + - - +
105A LYS* 3.1 28.4 + - - +
106A PHE* 3.7 14.9 - - - -
334A ARG* 5.5 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A VAL 3.8 0.8 + - - -
101A VAL 3.3 11.1 + - - -
102A ARG 3.2 4.7 - - - -
103A SER* 1.3 79.5 + - - +
105A LYS* 1.3 60.5 + - - +
106A PHE 3.5 2.9 + - - -
107A ASN* 3.9 24.9 + - - +
82B THR* 5.7 4.2 - - - +
----------------------------------------------------------
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