Contacts of the helix formed by residues 97 - 111 (chain B) in PDB entry 3GSB
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 CYS 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 5.1 1.5 - - - +
43A VAL* 3.6 11.2 - - - -
44A PHE 4.2 3.4 - - - +
93B PHE* 3.9 26.5 - - + -
95B ALA 4.7 0.9 - - - +
96B PRO* 1.3 77.1 - - - +
98B ALA* 1.3 63.7 + - - +
99B LEU* 3.6 15.3 - - + +
100B GLU* 3.1 47.3 + - - +
101B ASN* 4.2 5.7 + - - +
308B GLY 4.0 9.0 - - - -
310B PRO* 4.9 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.3 29.4 - - + -
43A VAL* 3.8 7.2 - - + +
44A PHE 4.9 1.6 + - - -
55A VAL* 5.7 3.1 - - + -
97B CYS* 1.3 72.3 - - - +
99B LEU* 1.3 67.2 + - + +
101B ASN* 3.2 13.4 + - + +
102B VAL* 3.2 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 5.7 2.7 - - + -
97B CYS* 3.2 11.7 + - + +
98B ALA* 1.3 81.7 - - + +
100B GLU* 1.3 56.9 + - - +
102B VAL* 3.3 15.5 + - + +
103B LEU* 2.8 31.0 + - - +
310B PRO* 4.2 19.1 - - + +
313B MET* 3.7 19.3 - - + -
314B THR* 3.6 23.3 - - - +
317B ILE* 4.1 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A MET* 3.6 21.3 - - + +
27A VAL* 6.0 0.8 - - - -
28A SER* 2.8 36.9 + - - +
32A ARG* 3.6 7.4 + - - -
95B ALA 4.3 0.4 - - - +
96B PRO* 3.4 13.2 - - - +
97B CYS* 3.1 34.3 + - - +
98B ALA 3.3 1.0 - - - -
99B LEU* 1.3 75.8 - - - +
101B ASN* 1.3 52.4 + - - +
104B ALA* 2.8 36.2 + - - +
119B PHE* 3.7 3.6 - - - -
308B GLY* 3.3 28.6 - - - +
313B MET* 3.2 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.5 24.1 + - + +
18A ALA* 3.6 13.3 - - - +
19A ALA* 3.3 44.2 - - - +
22A LEU* 3.7 16.7 - - + +
23A MET* 3.7 7.3 - - - +
97B CYS 4.6 4.0 - - - +
98B ALA* 3.2 11.8 + - + +
100B GLU* 1.3 75.4 - - - +
102B VAL* 1.3 66.7 + - - +
104B ALA* 3.6 0.5 - - - +
105B GLU* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 3.2 18.8 - - + +
99B LEU* 3.3 26.7 - - + +
101B ASN* 1.3 79.4 - - - +
103B LEU* 1.3 63.3 + - - +
105B GLU* 3.7 8.4 - - - +
106B MET* 3.1 37.9 + - + +
317B ILE* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU 2.8 20.8 + - - +
102B VAL* 1.3 71.2 - - - +
104B ALA* 1.3 67.8 + - - +
106B MET* 3.0 17.1 + - + +
107B VAL* 3.1 21.8 + - + +
119B PHE* 3.6 28.3 - - + -
275B ILE* 4.3 22.7 - - + +
281B VAL* 5.9 2.5 - - + -
312B ALA 5.2 0.2 - - - +
313B MET* 3.7 35.7 - - + +
316B GLY 4.5 4.0 - - - +
317B ILE* 3.9 33.6 - - + +
320B LEU* 4.9 4.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
22A LEU* 4.2 20.2 - - + -
23A MET* 4.2 6.5 - - + -
100B GLU 2.8 23.2 + - - +
101B ASN* 3.6 3.8 - - - +
103B LEU* 1.3 70.7 - - - +
105B GLU* 1.3 64.6 + - - +
107B VAL* 2.9 15.2 + - - +
108B ASN* 3.0 17.7 + - - +
117B VAL* 3.9 20.0 - - + -
119B PHE* 3.7 15.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.4 26.2 - - + +
101B ASN 2.9 21.5 + - - +
102B VAL* 3.7 8.1 - - - +
104B ALA* 1.3 72.2 - - - +
106B MET* 1.3 62.7 + - + +
108B ASN* 3.4 6.3 + - + +
109B ASP* 3.2 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 3.1 25.9 + - + +
103B LEU* 3.0 9.3 + - + +
104B ALA 3.0 0.2 + - - -
105B GLU* 1.3 76.5 - - + +
107B VAL* 1.3 59.0 + - - +
109B ASP* 3.3 10.5 + - - +
110B ALA* 3.0 28.1 + - - +
255B TYR* 5.1 4.1 + - - +
317B ILE* 3.9 36.8 - - + -
320B LEU* 4.6 17.8 - - + +
321B GLU* 4.6 6.1 - - + +
324B ARG* 3.5 39.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.1 15.7 + - + +
104B ALA* 2.9 10.9 + - - +
106B MET* 1.3 77.1 - - - +
108B ASN* 1.3 64.7 + - - +
110B ALA* 4.4 5.4 - - - -
111B VAL* 3.1 26.1 + - + +
114B ILE* 4.1 4.8 - - + +
117B VAL* 3.8 27.4 - - + -
119B PHE* 4.9 3.6 - - + -
251B PHE* 4.3 13.2 - - + -
271B LEU* 3.8 22.0 - - + -
275B ILE* 3.6 31.4 - - + -
320B LEU* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS 5.0 0.4 + - - -
22A LEU* 4.3 22.6 + - - +
104B ALA 3.0 17.8 + - - +
105B GLU* 3.8 7.2 - - - +
107B VAL* 1.3 75.0 - - - +
109B ASP* 1.3 65.2 + - - +
111B VAL 3.3 16.8 - - - +
112B PRO 4.9 0.3 - - - +
114B ILE* 3.4 25.8 - - - +
115B GLU* 3.2 26.6 + - - +
116B MET* 4.0 4.0 - - - +
117B VAL* 3.6 18.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
105B GLU* 3.2 20.9 + - - +
106B MET* 3.4 11.8 - - - +
108B ASN* 1.3 84.2 - - - +
110B ALA* 1.3 62.9 + - - +
111B VAL 4.8 1.6 - - - -
255B TYR* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MET 3.0 15.6 + - - +
107B VAL* 3.4 4.5 + - - +
109B ASP* 1.3 79.2 - - - +
111B VAL* 1.3 58.9 + - - +
112B PRO* 3.6 5.5 - - - +
251B PHE* 3.7 25.8 - - + -
255B TYR* 3.5 36.0 - - + +
256B GLY* 3.3 19.8 + - - -
260B GLU* 4.3 5.9 - - - +
320B LEU* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 3.1 22.6 + - + +
108B ASN 3.3 15.3 - - - +
109B ASP 4.8 1.6 - - - -
110B ALA* 1.3 80.2 - - + +
112B PRO* 1.3 73.3 - - + +
113B SER* 3.5 22.0 - - - +
114B ILE* 3.3 36.5 + - + +
251B PHE* 4.9 6.5 - - + -
255B TYR 5.6 0.4 - - - +
256B GLY* 4.5 10.5 - - - +
259B GLN* 3.7 16.6 - - - +
269B THR* 4.1 2.0 - - + +
271B LEU* 4.4 12.1 - - + -
----------------------------------------------------------
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