Contacts of the helix formed by residues 99 - 108 (chain C) in PDB entry 1YFJ
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 99 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ARG* 2.8 35.1 + - - -
94C TYR* 3.2 15.4 - - - -
97C THR* 3.2 17.4 + - - +
98C ARG* 1.3 75.0 - - - +
100C PRO* 1.3 62.5 - - - +
101C LEU* 2.8 16.4 + - - +
102C LEU* 2.9 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PRO 5.3 0.7 - - - +
57C GLU* 3.8 21.5 - - + +
58C MET* 3.5 34.1 - - + +
61C ARG* 3.7 21.5 - - + +
62C LEU* 6.4 0.2 - - - -
94C TYR* 4.6 2.5 - - + +
98C ARG 3.2 10.3 - - - +
99C ASP* 1.3 90.1 - - - +
101C LEU* 1.3 58.5 + - - +
103C LEU* 3.1 13.0 + - + +
104C TYR 3.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ARG* 3.3 35.2 - - + +
62C LEU* 4.8 3.1 - - + -
65C VAL* 4.6 15.3 - - + -
69C ASP* 4.8 15.3 - - + +
70C VAL* 4.3 23.3 - - + -
73C VAL* 3.9 26.0 - - + -
99C ASP* 2.8 21.4 + - - +
100C PRO* 1.3 74.6 - - - +
102C LEU* 1.3 61.3 + - + +
104C TYR* 3.5 9.9 + - + +
105C VAL* 3.3 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C VAL* 3.8 25.1 - - + -
77C TYR* 4.2 18.6 - - + +
90C LEU* 3.4 23.7 - - + +
93C ASP* 4.3 3.8 - - + -
94C TYR* 4.0 26.9 - - + +
97C THR* 3.9 13.7 - - + +
99C ASP* 2.9 32.6 + - + +
101C LEU* 1.3 77.2 - - + +
103C LEU* 1.3 57.0 + - - +
105C VAL* 3.9 2.8 - - - +
106C LEU* 2.7 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PRO* 3.5 45.1 - - + +
55C ILE* 4.3 3.1 - - + +
58C MET* 4.0 13.7 - - + -
94C TYR* 3.7 33.3 - - + +
99C ASP 3.4 2.6 + - - -
100C PRO* 3.1 11.5 + - + +
102C LEU* 1.3 79.6 - - - +
104C TYR* 1.3 62.6 + - - +
106C LEU* 3.2 5.3 + - + +
107C HIS* 2.9 22.2 + - - +
115C ILE* 4.3 17.0 - - + -
117C ILE* 4.8 0.9 - - + -
123C PHE* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ALA 4.6 5.0 + - - -
5C ILE* 4.0 17.3 - - + -
58C MET* 3.5 28.9 - - + -
62C LEU* 3.6 38.8 - - + +
67C TRP* 4.0 1.6 - + - -
70C VAL* 3.9 30.1 - - + -
100C PRO 3.1 6.9 + - - +
101C LEU* 3.6 11.2 - - + +
103C LEU* 1.3 79.2 - - - +
105C VAL* 1.3 66.0 + - - +
107C HIS* 2.9 29.4 + + - -
108C PHE* 3.3 38.0 + + - -
136C SER 4.3 1.0 + - - -
139C ARG* 5.6 0.2 - - - +
140C PHE* 3.3 35.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C VAL* 3.9 24.2 - - + +
73C VAL* 3.7 33.9 - - + -
74C ILE* 4.0 7.2 - - + -
79C LEU* 3.8 16.2 - - + -
90C LEU* 3.8 18.8 - - + -
101C LEU* 3.3 19.7 + - + +
102C LEU 3.9 3.4 - - - +
104C TYR* 1.3 76.4 - - - +
106C LEU* 1.3 61.8 + - - +
108C PHE* 3.4 12.1 + - - +
109C HIS* 2.7 33.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 3.4 36.8 - - + -
90C LEU* 4.0 22.7 - - + +
91C ARG* 4.0 17.5 - - - -
94C TYR* 3.9 27.4 - - + -
102C LEU 2.7 22.3 + - - +
103C LEU* 3.3 6.1 - - + +
105C VAL* 1.3 73.1 - - - +
107C HIS* 1.3 53.1 + - - +
109C HIS* 2.6 34.7 + - - +
110C GLY 3.6 4.2 + - - -
123C PHE* 3.3 41.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 3.5 38.8 - - + +
6C ALA* 4.1 11.5 + - - +
58C MET* 5.8 0.4 - - - -
103C LEU 2.9 13.5 + - - +
104C TYR* 2.9 26.6 + + - +
106C LEU* 1.3 74.6 - - - +
108C PHE* 1.3 101.2 + + - +
109C HIS 3.1 1.2 + - - -
110C GLY 3.6 7.5 + - - +
113C ASN* 3.7 36.3 + - + +
115C ILE* 3.7 32.5 - - + -
123C PHE* 4.5 7.4 - - - -
139C ARG* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C TRP* 4.3 6.3 - + - -
70C VAL* 4.5 4.9 - - + -
74C ILE* 5.3 0.7 - - + -
104C TYR* 3.3 61.0 - + - -
105C VAL* 3.4 15.4 + - - +
106C LEU 2.9 1.2 + - - -
107C HIS* 1.3 98.4 + + - +
109C HIS* 1.3 70.1 + + + +
113C ASN* 4.1 7.9 - - - +
130C ARG* 3.6 18.0 - - - +
131C THR* 3.7 13.6 + - - +
132C ILE* 3.5 24.2 - - + +
136C SER* 3.6 39.0 - - - -
139C ARG* 5.6 5.8 - - + -
----------------------------------------------------------
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