Contacts of the helix formed by residues 99 - 107 (chain B) in PDB entry 4FZY
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 THR 99 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.6 26.2 - - + -
79B ALA 3.2 5.0 + - - -
80B HIS* 2.9 39.2 + - - +
97B ILE 4.0 0.6 + - - -
98B CYS* 1.3 71.0 - - - +
100B MET* 1.3 55.4 + - - +
102B LEU* 3.8 8.7 - - + -
103B ALA* 2.9 30.5 + - - +
143B THR* 3.6 18.8 - - + +
146B LEU* 4.1 10.4 - - - +
147B LEU* 4.1 20.4 - - + +
150B ILE* 3.8 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B HIS* 3.6 17.9 + - + -
81B ASN* 3.5 31.2 - - - +
98B CYS* 3.1 14.9 - - - -
99B THR* 1.3 78.8 + - - +
101B LYS* 1.3 66.7 + - + +
103B ALA* 3.2 5.6 + - - +
104B ARG* 3.1 43.8 + - - +
112B TYR* 4.1 20.6 - - + +
117B LEU* 5.4 0.2 - - - -
9D T 5.9 1.1 - - - +
10D A 3.4 42.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B CYS* 3.2 22.6 + - + +
100B MET* 1.3 81.4 - - + +
102B LEU* 1.3 61.7 + - + +
104B ARG* 3.5 13.9 + - + +
105B ARG* 3.2 29.9 + - - +
164B ILE* 3.0 37.4 - - + +
165B THR* 4.1 17.2 + - - +
166B GLY 4.8 5.1 + - - -
5C G 4.4 3.6 + - - -
6C A 3.2 31.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
97B ILE* 3.7 23.6 - - + -
98B CYS 3.2 16.9 + - - +
99B THR* 3.9 11.2 - - - +
101B LYS* 1.3 76.0 - - + +
103B ALA* 1.3 64.4 + - - +
105B ARG* 3.6 6.9 + - - +
106B LEU* 3.1 27.7 + - - +
147B LEU* 4.7 3.1 - - + -
150B ILE* 4.0 21.8 - - + -
156B TRP* 4.2 9.3 - - + -
161B MET* 3.9 31.9 - - - +
164B ILE* 3.9 40.8 - - + -
165B THR* 4.9 1.8 - - - +
----------------------------------------------------------
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 THR 2.9 19.5 + - - +
100B MET 3.2 5.1 + - - +
102B LEU* 1.3 76.4 - - - +
104B ARG* 1.3 57.8 + - - +
107B TRP* 2.8 58.6 + - + +
112B TYR* 3.9 6.4 - - + -
117B LEU* 3.9 28.0 - - + -
146B LEU* 5.1 1.3 - - + -
150B ILE* 4.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B MET* 3.1 35.6 + - - +
101B LYS* 3.7 15.6 - - + +
103B ALA* 1.3 77.8 - - - +
105B ARG* 1.3 67.3 + - - +
106B LEU 3.2 0.5 + - - -
107B TRP 3.4 6.1 + - - -
108B PRO* 3.5 17.8 - - - +
112B TYR* 3.4 47.2 - - + +
5C G 5.8 3.2 - - - +
6C A 4.6 28.5 + - - -
7C T 4.7 18.0 + - - -
9D T 5.2 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS* 3.2 21.4 + - - +
102B LEU* 3.8 8.7 - - - +
103B ALA 3.5 0.2 - - - -
104B ARG* 1.3 78.3 - - - +
106B LEU* 1.3 62.6 + - + +
108B PRO* 4.1 8.7 - - - +
156B TRP* 3.4 31.7 - - + -
164B ILE* 3.9 37.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU 3.1 12.4 + - - +
103B ALA 3.9 0.2 - - - +
105B ARG* 1.3 84.8 - - + +
107B TRP* 1.3 100.2 + - + +
108B PRO* 3.4 7.8 - - - +
150B ILE* 3.8 38.4 - - + +
153B THR* 4.2 13.9 - - + -
154B SER* 4.2 8.1 - - - -
156B TRP* 3.3 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA* 2.8 39.0 + - + +
104B ARG 3.4 2.9 + - - -
106B LEU* 1.3 97.2 + - + +
108B PRO* 1.3 58.5 - - - +
110B ILE* 3.2 24.1 - - + +
112B TYR* 2.7 24.6 + - - -
117B LEU* 5.1 7.2 - - + -
121B ARG* 3.3 51.8 - - + +
146B LEU* 4.2 10.3 - - + -
149B ASP* 3.7 17.5 - - - -
150B ILE* 3.8 31.9 - - + -
153B THR* 4.0 21.5 - - - +
----------------------------------------------------------
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