Contacts of the helix formed by residues 93 - 111 (chain U) in PDB entry 3J9X
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 93 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64S THR 4.6 0.2 - - - -
92U SER* 1.3 77.4 - - - +
94U PRO* 1.3 67.8 - - - -
95U ALA 3.3 1.8 - - - -
96U LEU* 2.7 30.0 + - - +
97U VAL* 3.1 14.9 + - - +
133U VAL* 4.3 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 94 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64S THR* 3.3 17.3 - - + +
65S GLN* 3.4 26.9 - - + +
66S TYR 4.6 0.4 - - - -
67S GLY* 3.8 11.9 - - - +
92U SER 4.6 0.7 - - - +
93U GLY* 1.3 83.7 - - - -
95U ALA* 1.3 63.4 + - - +
97U VAL* 3.0 11.7 + - + +
98U ASN* 2.9 25.4 + - - +
133U VAL* 4.3 9.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64S THR* 3.3 19.0 + - + +
67S GLY* 3.5 16.4 - - - -
68S ILE 3.7 20.2 - - - +
69S THR* 3.4 13.6 - - + +
90U ILE* 3.5 25.7 - - + +
93U GLY 3.1 0.4 + - - -
94U PRO* 1.3 80.4 - - - +
96U LEU* 1.3 61.9 + - - +
98U ASN* 3.3 1.9 + - - +
99U MET* 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83U VAL* 4.3 6.3 - - + +
86U ALA* 3.9 28.9 - - + +
87U LEU* 3.8 37.7 - - + +
90U ILE* 4.2 4.7 - - + +
91U GLY 3.6 12.8 + - - +
92U SER* 3.9 10.8 - - - -
93U GLY 2.7 16.7 + - - +
95U ALA* 1.3 71.3 - - - +
97U VAL* 1.3 62.4 + - + +
99U MET* 3.1 5.5 + - + +
100U ILE* 2.8 51.2 + - + +
126U THR* 4.6 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93U GLY 3.1 7.6 + - - +
94U PRO* 3.0 10.3 + - + +
96U LEU* 1.3 78.7 - - + +
98U ASN* 1.3 67.5 + - - +
100U ILE* 3.3 0.6 + - + -
101U ASN* 3.1 33.1 + - - +
130U THR* 3.4 25.9 + - - +
131U GLY* 3.5 29.6 - - - +
132U TYR 4.8 2.9 - - - +
133U VAL* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 98 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67S GLY* 3.1 35.6 + - - -
69S THR* 4.4 7.6 - - + -
94U PRO* 2.9 13.6 + - - +
95U ALA* 3.5 7.9 - - - +
96U LEU 3.2 0.2 - - - -
97U VAL* 1.3 81.6 - - - +
99U MET* 1.3 62.5 + - - +
101U ASN* 3.5 8.5 + - - +
102U GLY 3.3 15.4 + - - -
109V SER 3.5 23.1 - - - +
110V ALA* 3.7 4.0 - - - +
112V ASN* 5.2 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248 T 4.1 11.4 - - - +
69S THR* 4.6 5.6 - - + -
82U LYS* 4.7 12.1 - - + -
83U VAL* 6.3 0.2 - - - -
86U ALA* 3.8 25.4 - - + -
90U ILE* 3.7 22.4 - - + -
95U ALA 3.0 14.4 + - - +
96U LEU* 3.1 13.7 + - + +
98U ASN* 1.3 76.3 - - - +
100U ILE* 1.3 60.3 + - + +
102U GLY* 3.2 3.3 + - - -
103U LEU* 2.8 32.9 + - + +
106V TYR* 4.7 9.2 - - - -
110V ALA* 4.2 20.3 + - - +
111V PHE* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79U PHE* 5.0 3.1 - - + -
83U VAL* 4.3 18.6 - - + -
96U LEU* 2.8 47.9 + - + +
97U VAL 3.9 3.1 - - - +
99U MET* 1.3 73.7 - - + +
101U ASN* 1.3 57.9 + - - +
103U LEU* 3.5 7.9 - - + +
104U LYS* 2.8 44.1 + - + +
122U VAL* 4.2 15.7 - - + -
126U THR* 4.1 22.7 - - + -
130U THR* 3.5 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97U VAL* 3.1 32.9 + - - +
98U ASN* 3.7 10.1 + - - +
99U MET 3.2 0.2 - - - -
100U ILE* 1.3 77.9 - - - +
102U GLY* 1.3 62.2 + - - +
104U LYS* 3.5 8.8 + - - +
105U GLY* 3.2 17.2 + - - -
130U THR* 3.3 20.2 - - - +
131U GLY* 4.3 8.0 + - - -
109V SER* 4.2 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98U ASN 3.3 4.9 + - - -
99U MET 3.2 5.6 + - - -
101U ASN* 1.3 75.8 - - - +
103U LEU* 1.3 60.0 + - - +
105U GLY* 3.1 3.8 + - - -
106U TYR 2.9 24.1 + - - -
105V GLY 5.3 0.2 - - - -
106V TYR* 3.5 20.1 - - - -
109V SER* 3.0 24.3 + - - -
110V ALA* 4.0 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79U PHE* 3.6 17.0 - - + -
82U LYS* 3.5 46.7 - - + +
83U VAL* 3.6 31.4 - - + +
99U MET* 2.8 22.7 + - + +
100U ILE* 3.2 9.2 + - + +
102U GLY* 1.3 74.0 - - - +
104U LYS* 1.3 66.3 + - - +
106U TYR* 3.1 12.0 + - + +
107U TYR* 3.0 41.0 + - + -
106V TYR* 3.9 9.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79U PHE* 3.8 29.2 - - + -
100U ILE* 2.8 32.8 + - + +
101U ASN* 3.7 7.7 + - - +
103U LEU* 1.3 75.0 - - - +
105U GLY* 1.3 57.9 + - - +
107U TYR* 3.2 1.6 + - - +
108U ILE* 2.8 54.7 + - + +
115U PRO* 5.0 5.5 - - - +
118U LEU* 4.8 6.1 - - + -
119U ASP* 2.7 36.9 + - - +
122U VAL* 5.0 2.0 - - + -
129U PRO* 6.1 0.2 - - - +
130U THR* 4.6 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101U ASN 3.2 8.3 + - - -
102U GLY* 3.1 8.4 + - - -
104U LYS* 1.3 77.7 - - - +
106U TYR* 1.3 58.2 + - - +
108U ILE* 4.5 6.0 - - - +
109U SER* 2.6 37.3 + - - -
102V GLY 4.4 3.4 - - - -
105V GLY* 5.9 1.8 - - - -
106V TYR 5.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2157 A 3.8 5.0 + - - -
2167 T 2.9 18.0 + - - -
82U LYS* 5.6 3.8 - - - -
102U GLY 2.9 12.9 + - - +
103U LEU* 3.2 16.6 - - + +
105U GLY* 1.3 74.5 - - - +
107U TYR* 1.3 84.9 + + - +
110U ALA* 2.8 41.5 + - + +
111U PHE* 3.7 27.2 - + - -
82V LYS* 2.8 40.7 + - - -
99V MET* 4.6 8.0 - - - +
102V GLY 3.7 14.1 + - - -
103V LEU* 4.0 12.6 - - + -
106V TYR* 3.7 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2157 A 4.5 5.2 - - + +
2167 T 3.3 33.5 + - - -
75U ILE* 3.5 38.8 - - + -
78U GLY* 3.5 10.1 - - - -
79U PHE* 3.7 30.3 - + + -
82U LYS* 5.2 1.6 - - + -
103U LEU* 3.0 26.2 + - + +
104U LYS 4.0 2.0 - - - +
106U TYR* 1.3 98.5 - + - +
108U ILE* 1.3 64.3 + - - +
111U PHE* 3.1 40.2 + + + -
113U ALA* 3.0 26.1 + - + +
118U LEU* 4.4 7.9 - - + -
71X PRO* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104U LYS* 2.8 44.3 + - + +
105U GLY* 4.1 5.4 - - - +
107U TYR* 1.3 72.3 - - - +
109U SER* 1.3 61.8 + - - +
112U ASN* 3.1 24.9 - - - +
113U ALA 3.6 16.3 + - - +
115U PRO* 3.9 31.4 - - + -
118U LEU* 3.3 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105U GLY 2.6 21.5 + - - -
108U ILE* 1.3 84.0 - - - +
110U ALA* 1.3 61.0 + - - +
111U PHE 3.5 0.2 - - - -
112U ASN* 4.0 10.2 - - - +
98V ASN* 3.5 17.5 - - - +
101V ASN* 4.2 5.9 - - - +
102V GLY* 2.9 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106U TYR* 2.8 26.1 + - + +
109U SER* 1.3 78.9 + - - +
111U PHE* 1.3 62.2 + - + +
112U ASN* 3.6 1.7 + - - -
98V ASN* 3.6 12.8 - - - +
99V MET* 3.9 35.2 + - - +
102V GLY* 4.1 4.7 - - - -
69X THR* 2.6 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2157 A 3.8 24.9 - - - -
75U ILE* 4.8 13.4 - - + +
106U TYR* 3.7 34.5 - + - -
107U TYR* 3.1 47.4 + + + +
110U ALA* 1.3 78.9 - - + +
112U ASN* 1.3 75.5 + - - +
113U ALA* 3.2 2.6 + - - +
99V MET* 3.7 27.1 - - + -
69X THR* 3.4 16.8 - - - +
70X GLY* 3.5 31.2 - - - -
71X PRO* 4.6 3.6 - - + -
72X ASN* 3.3 19.0 + - - +
----------------------------------------------------------
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