Contacts of the helix formed by residues 99 - 109 (chain C) in PDB entry 6UZA
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 GLU 99 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ARG* 5.3 3.3 + - - -
95C LEU* 3.8 22.6 - - + +
96C SER* 3.5 29.1 + - - +
97C ILE 3.4 0.4 - - - -
98C GLU* 1.3 81.0 - - - +
100C GLU* 1.3 61.4 + - - +
101C ARG 3.2 1.3 - - - -
102C PHE* 3.7 5.8 - - - +
103C LEU* 2.9 32.7 + - - +
123C SER 5.1 3.6 - - - +
124C LEU* 4.3 11.5 - - + +
125C ASN* 4.0 20.1 + - - +
128C CYS* 3.7 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU* 4.5 18.0 - - + +
96C SER 3.2 17.4 + - - +
97C ILE* 4.9 4.7 - - + +
99C GLU* 1.3 73.9 - - - +
101C ARG* 1.3 58.5 + - + +
103C LEU* 3.5 5.1 + - - +
104C ASP* 2.9 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ILE* 3.4 23.4 + - + +
98C GLU* 4.7 6.2 - - - +
99C GLU 3.2 0.4 - - - -
100C GLU* 1.3 78.0 - - + +
102C PHE* 1.3 56.3 + - - +
104C ASP* 3.4 5.4 + - - +
105C ALA* 2.9 31.0 + - - +
113C VAL* 3.9 18.8 - - + +
116C LYS* 3.1 27.9 - - - +
117C MET* 3.4 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLU 4.2 4.7 - - - +
99C GLU* 3.3 8.5 + - - +
101C ARG* 1.3 79.1 - - - +
103C LEU* 1.3 59.2 + - + +
105C ALA* 3.4 2.2 + - - +
106C ALA* 2.9 28.5 + - + +
114C VAL* 4.1 27.6 - - + -
117C MET* 3.7 35.5 - - + +
118C LEU* 3.8 30.1 - - + -
124C LEU* 4.3 15.5 - - + -
125C ASN 4.8 0.2 - - - -
126C VAL* 4.3 21.8 - - + -
128C CYS* 4.4 16.6 - - - -
136C ALA* 3.7 25.1 - - + -
152C LEU* 3.9 15.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
95C LEU* 3.9 24.0 - - + -
99C GLU 2.9 18.8 + - - +
100C GLU* 4.0 4.5 - - - +
101C ARG 3.3 0.2 - - - -
102C PHE* 1.3 75.8 - - + +
104C ASP* 1.3 61.2 - - - +
106C ALA* 3.8 2.2 - - - +
107C GLU* 2.9 32.3 + - - +
128C CYS* 3.8 27.6 - - - +
129C VAL 3.8 28.9 - - - +
130C ASP* 3.9 10.8 - - + +
134C GLN 4.4 1.1 - - - +
135C ASN 4.3 1.1 - - - -
136C ALA* 4.2 22.4 - - + +
139C LEU* 4.0 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 5.6 4.5 + - - +
100C GLU* 2.9 25.9 + - - +
101C ARG* 3.9 5.6 - - - +
103C LEU* 1.3 79.0 - - - +
105C ALA* 1.3 56.9 + - - +
107C GLU* 4.6 4.3 - - - +
108C TYR* 2.9 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ARG 2.9 18.6 + - - +
102C PHE* 3.8 4.5 - - + +
104C ASP* 1.3 77.3 - - - +
106C ALA* 1.3 63.1 + - - +
109C GLY 3.3 3.5 + - - -
110C ASN* 2.9 41.6 + - + +
113C VAL* 3.8 23.1 - - + -
114C VAL* 3.8 19.3 - - + -
148C ILE* 3.6 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PHE* 2.9 19.7 + - + +
103C LEU* 3.9 4.0 - - - +
105C ALA* 1.3 77.1 - - - +
107C GLU* 1.3 63.0 + - - +
114C VAL* 4.1 5.8 - - + +
136C ALA* 3.7 37.2 - - + +
139C LEU* 4.8 3.1 - - + -
140C ALA* 3.9 10.4 - - - -
145C HIS* 3.6 15.9 - - - -
148C ILE* 3.9 20.1 - - + +
152C LEU* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLU* 5.5 4.3 - - - +
103C LEU 2.9 18.1 + - - +
104C ASP* 4.1 5.7 - - - +
105C ALA 3.3 0.2 - - - -
106C ALA* 1.3 77.9 - - - +
108C TYR* 1.3 91.2 + - + +
130C ASP* 5.6 1.2 - - - +
139C LEU* 4.2 30.1 - - + +
143C ASN* 3.4 29.3 + - - +
145C HIS* 3.0 18.0 + - - -
889C GLN* 3.4 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 5.1 8.7 - - - +
175B ARG* 3.7 62.1 - - + +
233B GLU* 5.2 5.2 + - - -
104C ASP* 2.9 42.0 + - + +
107C GLU* 1.3 108.9 + - + +
109C GLY* 1.3 60.1 + - - +
110C ASN* 3.6 2.0 - - + +
145C HIS* 3.8 3.3 + - - -
889C GLN* 3.7 23.5 - - - +
892C SER* 3.0 27.4 + - - +
893C SER 4.5 0.2 + - - -
896C TYR* 3.6 10.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ALA 3.3 4.4 + - - -
107C GLU 3.4 3.6 - - - -
108C TYR* 1.3 79.6 - - - +
110C ASN* 1.3 59.8 + - - +
111C ILE* 2.9 19.9 + - - +
145C HIS* 3.5 22.8 + - - -
148C ILE* 3.7 12.6 - - - -
893C SER* 3.7 17.7 - - - -
896C TYR* 4.0 6.3 - - - +
----------------------------------------------------------
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