Contacts of the helix formed by residues 105 - 117 (chain B) in PDB entry 5SWW
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 105 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 5.5 1.3 - - - -
102B PHE 3.1 13.6 + - - -
103B SER 3.5 1.2 + - - -
104B TRP* 1.3 78.1 - - - +
106B CYS* 1.3 64.6 + - - +
107B ALA 3.5 2.2 - - - -
108B GLY* 3.5 6.2 + - - -
109B GLU* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B HIS* 3.5 19.5 - - - -
72B ALA* 4.0 17.9 - - + -
73B LEU* 3.9 24.7 - - - -
100B PRO* 4.6 2.7 - - + -
101B CYS* 3.8 11.3 + - - +
104B TRP 3.4 2.6 - - - -
105B GLY* 1.3 76.8 - - - +
107B ALA* 1.3 60.0 + - - +
109B GLU* 3.2 5.7 + - - +
110B VAL* 2.9 35.2 + - - +
201B ZN 2.2 35.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PRO* 4.9 3.3 - - + +
101B CYS 3.1 21.0 + - - +
102B PHE* 4.5 5.8 - - + +
105B GLY 3.5 0.4 - - - -
106B CYS* 1.3 74.8 - - - +
108B GLY* 1.3 58.5 + - - +
110B VAL* 3.4 2.0 + - - +
111B ARG* 2.9 28.9 + - - +
139B ALA* 3.9 31.9 - - + +
142B MET* 3.9 13.5 - - - +
143B LEU* 4.3 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 5.4 3.2 + - - -
105B GLY* 3.5 8.1 + - - -
106B CYS 3.2 0.4 - - - -
107B ALA* 1.3 79.2 - - - +
109B GLU* 1.3 60.2 + - - +
111B ARG* 3.3 11.6 + - - +
112B ALA* 2.9 27.9 + - - +
142B MET* 3.8 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.8 28.4 - - + +
76B LEU* 3.9 9.4 - - + +
105B GLY* 3.0 24.3 + - - +
106B CYS 3.8 2.7 - - - +
108B GLY* 1.3 74.5 - - - +
110B VAL* 1.3 61.8 + - - +
112B ALA* 3.2 10.5 + - - +
113B PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 4.3 8.5 - - + -
76B LEU* 4.1 19.5 - - + -
94B TRP* 3.9 24.5 - - + -
100B PRO* 5.7 1.8 - - + -
106B CYS 2.9 22.3 + - - +
107B ALA* 3.8 4.0 - - - +
109B GLU* 1.3 76.6 - - - +
111B ARG* 1.3 57.6 + - - +
113B PHE* 3.2 5.8 + - + +
114B LEU* 2.9 36.3 + - + +
122B LEU* 3.8 26.2 - - + -
143B LEU* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ALA 2.9 18.0 + - - +
108B GLY* 3.6 9.9 + - - +
110B VAL* 1.3 77.7 - - - +
112B ALA* 1.3 60.3 + - - +
114B LEU* 3.3 2.4 + - - +
115B GLN* 3.1 46.5 + - - +
142B MET* 3.4 48.6 - - + +
143B LEU* 5.1 1.5 - - + +
145B ASP* 6.0 1.1 - - - -
146B ALA* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 2.9 14.2 + - - +
109B GLU* 3.2 17.5 + - - +
111B ARG* 1.3 77.2 - - - +
113B PHE* 1.3 61.6 + - - +
115B GLN* 3.3 9.2 + - - +
116B GLU* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 5.6 4.7 - + - -
76B LEU* 4.0 29.6 - - + -
79B VAL* 3.6 40.6 - - + -
84B LEU* 5.3 0.7 - - + -
92B VAL* 6.0 1.1 - - + -
109B GLU 2.9 13.7 + - - +
110B VAL* 3.6 8.5 - - + +
112B ALA* 1.3 76.1 - - - +
114B LEU* 1.3 72.1 + - + +
116B GLU* 4.7 2.0 - - - -
117B ASN* 2.9 64.0 + - + +
120B VAL* 4.1 29.8 - - + -
122B LEU* 6.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 2.9 32.5 + - + +
111B ARG* 3.8 4.7 - - - +
112B ALA 3.3 0.2 - - - -
113B PHE* 1.3 93.2 - - + +
115B GLN* 1.3 60.3 + - + +
117B ASN 3.2 17.9 - - - +
118B THR* 3.9 6.6 + - - +
120B VAL* 4.0 19.4 - - + +
121B ARG* 5.1 0.2 - - - -
122B LEU* 3.9 23.8 - - + +
143B LEU* 5.0 1.1 - - + +
146B ALA* 4.0 31.9 - - + +
147B GLY 5.0 0.7 - - - -
148B ALA* 3.7 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ARG* 3.1 44.8 + - + +
112B ALA* 3.9 6.7 - - - +
114B LEU* 1.3 79.2 - - + +
116B GLU* 1.3 65.0 + - - +
118B THR* 3.3 19.2 - - - +
146B ALA* 5.5 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA 3.0 16.8 + - - +
113B PHE* 4.1 1.6 - - - +
115B GLN* 1.3 80.1 - - - +
117B ASN* 1.3 71.3 + - - +
118B THR* 3.7 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 5.9 1.4 - - - +
84B LEU* 6.3 0.6 - - - +
113B PHE* 2.9 49.4 + - + +
114B LEU* 3.2 12.9 - - - +
116B GLU* 1.3 89.0 + - - +
118B THR* 1.3 63.9 + - - +
119B HIS* 3.2 35.7 + - + +
120B VAL* 3.5 19.2 + - + +
----------------------------------------------------------
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