Contacts of the helix formed by residues 98 - 111 (chain B) in PDB entry 3SZ9
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 98 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU 3.0 12.2 + - - +
95B ILE 3.1 5.4 + - - +
97B ARG* 1.3 119.8 + - - +
99B ARG* 1.3 62.0 + - - +
100B THR* 3.5 2.5 - - - -
101B TYR* 3.3 12.6 + - + +
102B LEU* 3.0 27.0 + - + +
203B TYR* 2.5 45.6 + - + -
207B LEU* 3.8 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE 3.0 9.4 + - - +
96B GLU* 3.3 29.3 + - - +
97B ARG 3.4 1.8 + - - -
98B ASP* 1.3 75.7 - - - +
100B THR* 1.3 60.0 + - + +
102B LEU 3.3 0.5 + - - -
103B ALA* 2.8 32.1 + - - +
118B TYR* 2.8 67.3 + - + -
119B LEU* 4.1 8.7 + - - +
122B LEU* 3.7 27.3 - - + +
123B ASP* 3.8 30.3 + - - +
126B LEU* 4.5 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 3.6 32.8 - - + -
10B ALA 5.0 5.6 - - - +
11B PRO* 5.5 1.8 - - - +
12B ASN 5.5 0.7 + - - -
97B ARG 5.3 2.3 + - - -
98B ASP 5.0 0.9 - - - -
99B ARG* 1.3 76.1 - - + +
101B TYR* 1.3 60.0 + - - +
104B ALA* 3.0 29.5 + - - +
114B TYR* 3.8 16.7 - - - +
118B TYR* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 6.3 3.6 - - + -
15B PRO* 3.6 23.6 - - + -
16B GLU 2.8 30.1 + - - -
17B VAL* 4.1 4.2 - - - -
18B PHE* 3.4 25.1 + + - -
98B ASP* 3.3 11.6 + - + +
99B ARG 3.2 0.6 - - - -
100B THR* 1.3 83.6 + - - +
102B LEU* 1.3 60.8 + - + +
104B ALA* 3.2 5.1 + - - +
105B LEU* 2.8 53.9 + - + +
203B TYR* 3.8 46.5 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 4.1 40.6 - - + +
98B ASP* 3.0 24.9 + - + +
99B ARG 4.0 2.5 - - - +
101B TYR* 1.3 78.2 - - + +
103B ALA* 1.3 61.6 + - - +
105B LEU* 3.8 2.6 - - + +
106B GLU* 2.8 30.8 + - - +
122B LEU* 4.1 13.5 - - + -
172B LEU* 4.1 18.5 - - + +
200B THR* 4.0 28.1 - - + +
203B TYR* 3.8 31.6 - - + -
204B VAL* 4.3 5.2 - - + -
207B LEU* 4.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG 2.8 18.0 + - - +
100B THR 3.9 0.2 - - - +
102B LEU* 1.3 77.5 - - - +
104B ALA* 1.3 61.3 + - - +
106B GLU* 3.4 0.6 + - - -
107B THR* 3.1 26.0 + - - -
114B TYR* 3.8 15.7 - - + -
117B SER* 3.5 9.4 - - - -
118B TYR* 3.7 37.5 - - + +
122B LEU* 3.8 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 3.4 33.0 - - + +
15B PRO* 4.1 9.9 - - + -
100B THR 3.0 18.8 + - - +
101B TYR* 3.2 5.6 + - - +
103B ALA* 1.3 75.4 - - - +
105B LEU* 1.3 58.0 + - - +
107B THR 3.3 1.0 + - - -
108B LEU* 2.9 26.0 + - - +
114B TYR* 3.7 15.1 - - + -
335B PHE* 3.4 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PRO* 4.0 20.1 - - + +
17B VAL* 4.4 13.7 - - + -
101B TYR* 2.8 48.3 + - + +
102B LEU* 3.8 5.8 - - + +
103B ALA 3.3 0.2 - - - -
104B ALA* 1.3 74.9 - - - +
106B GLU* 1.3 65.3 + - - +
108B LEU* 3.3 9.2 + - + +
109B ASP* 3.1 23.8 + - + +
199B LEU* 3.9 46.9 - - + +
200B THR* 3.7 15.0 - - + +
203B TYR* 4.6 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU 2.8 18.5 + - - +
103B ALA* 3.6 7.0 - - - +
105B LEU* 1.3 75.1 - - - +
107B THR* 1.3 57.9 + - - +
109B ASP* 3.9 1.6 - - - +
110B ASN* 2.9 36.0 + - + +
112B LYS* 4.2 15.5 - - + -
117B SER* 3.7 13.9 - - - +
121B ASP* 4.3 11.9 - - + +
122B LEU* 5.2 0.7 - - + -
170B PHE 4.4 0.2 - - - -
171B PRO* 3.4 25.8 - - + +
172B LEU* 3.0 36.7 + - + +
197B THR* 5.5 0.2 - - - -
200B THR* 2.8 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASN* 5.1 0.9 - - - +
42B PRO* 5.0 0.2 - - - +
43B SER* 5.4 0.5 + - - -
103B ALA 3.1 8.6 + - - -
104B ALA 3.6 6.7 - - - -
106B GLU* 1.3 77.2 - - - +
108B LEU* 1.3 64.6 + - - +
111B GLY* 2.9 22.8 + - - +
112B LYS 2.8 28.5 + - - +
114B TYR* 3.1 17.7 - - - +
117B SER* 3.1 15.3 + - - -
334B PRO* 3.6 26.0 - - + +
335B PHE* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN 3.5 24.0 - - - +
14B GLN* 4.2 9.0 - - - +
15B PRO* 4.1 25.6 - - + +
17B VAL* 5.5 0.2 - - + -
41B ASN* 3.2 49.1 - - - +
42B PRO* 3.5 3.6 - - - +
48B ILE* 3.7 33.2 - - + +
104B ALA 2.9 16.7 + - - +
105B LEU* 3.3 13.9 + - + +
107B THR* 1.3 78.5 - - - +
109B ASP* 1.3 58.4 + - - +
335B PHE* 3.9 12.5 - - + -
6911B EDO 3.5 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 2.6 12.8 + - - -
40B VAL 3.6 2.3 - - - +
42B PRO* 3.7 4.3 - - - +
48B ILE* 3.4 17.2 - - + +
105B LEU 3.1 16.0 + - - +
106B GLU* 4.3 2.0 - - - +
108B LEU* 1.3 77.7 - - + +
110B ASN* 1.3 59.3 + - - +
196B GLN 3.4 6.6 - - - +
197B THR* 3.4 9.3 - - + +
198B PRO* 3.1 24.6 - - - +
199B LEU* 3.4 24.3 + - + +
200B THR* 4.9 2.3 + - + -
345B VAL* 4.9 1.9 - - - +
601B NA 2.3 51.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO* 3.5 12.7 - - - +
106B GLU* 2.9 22.0 + - + +
109B ASP* 1.3 78.9 - - + +
111B GLY* 1.3 55.3 + - - +
112B LYS* 2.8 47.3 + - - +
168B TRP* 2.9 27.1 + - - -
169B ASN* 3.5 16.6 + - - +
171B PRO* 4.1 6.8 - - + +
197B THR* 3.9 13.6 - - + +
297B ASN* 4.5 1.6 + - - +
298B GLN* 4.6 2.4 + - - -
300B GLN* 4.9 7.6 + - - +
343B PRO 4.5 2.3 - - - +
345B VAL* 3.8 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO* 3.7 4.3 - - - +
43B SER* 4.8 2.5 - - - -
107B THR 2.9 14.1 + - - -
110B ASN* 1.3 77.3 - - - +
112B LYS* 1.3 67.2 + - - +
298B GLN* 4.4 4.3 - - - -
334B PRO* 3.2 15.2 - - - +
342B GLY* 3.5 3.3 - - - -
343B PRO* 3.3 37.2 - - - +
----------------------------------------------------------
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