Contacts of the helix formed by residues 79 - 93 (chain F) in PDB entry 5U0A
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 79 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F GLY 3.9 1.0 + - - -
78F TRP* 1.3 76.5 - - - +
80F ALA* 1.3 63.3 + - - +
81F ASP* 3.1 32.5 + - - +
82F LEU* 3.1 20.5 + - + +
83F ALA* 2.7 28.1 + - - +
135F ARG* 4.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ARG* 3.8 34.0 + - - +
78F TRP 3.9 0.8 + - - -
79F ASP* 1.3 79.5 + - - +
81F ASP* 1.3 63.7 + - - +
83F ALA* 3.2 2.9 + - - +
84F ASP* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ASP* 3.1 13.5 + - - +
80F ALA* 1.3 81.9 - - - +
82F LEU* 1.3 58.5 + - + +
84F ASP* 3.4 6.8 + - - +
85F ALA* 3.0 28.1 + - - +
142F ALA* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F TRP* 3.2 23.8 - - + -
79F ASP* 3.1 24.0 + - + +
81F ASP* 1.3 76.9 - - + +
83F ALA* 1.3 61.5 + - - +
85F ALA* 4.1 1.5 - - - +
86F GLY 2.9 23.0 + - - -
135F ARG* 4.4 28.0 - - + +
138F VAL* 4.4 4.8 - - + +
139F ALA* 4.1 35.0 - - + +
142F ALA* 4.3 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ALA* 3.8 27.1 - - - +
73F LEU* 3.9 17.8 - - + +
74F ARG* 4.0 11.0 - - - +
78F TRP* 3.9 10.5 - - + -
79F ASP 2.7 21.3 + - - +
80F ALA* 3.6 8.7 - - - +
82F LEU* 1.3 74.3 - - - +
84F ASP* 1.3 56.3 + - - +
86F GLY* 3.8 0.3 - - - -
87F ALA* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ILE* 4.4 2.3 - - - +
70F ALA* 4.7 8.0 - - + +
74F ARG* 5.7 1.8 - - - +
80F ALA 3.0 16.5 + - - +
81F ASP* 3.8 6.7 - - - +
82F LEU 3.3 0.2 - - - -
83F ALA* 1.3 77.9 - - - +
85F ALA* 1.3 57.4 + - - +
87F ALA* 3.4 4.6 + - - +
88F ARG* 3.0 51.1 + - - +
109F GLU 5.7 0.3 - - - -
110F ALA* 4.3 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F ASP 3.0 17.4 + - - +
82F LEU* 4.1 4.3 - - - +
84F ASP* 1.3 76.5 - - - +
86F GLY* 1.3 58.0 + - - +
88F ARG* 3.3 11.5 + - - +
89F GLN* 2.9 36.7 + - + +
138F VAL* 4.2 4.5 - - + -
142F ALA* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F LEU* 4.3 11.2 - - - -
78F TRP* 4.4 2.7 - - - -
82F LEU 2.9 18.2 + - - -
83F ALA 3.8 1.3 - - - -
85F ALA* 1.3 75.2 - - - +
87F ALA* 1.3 58.3 + - - +
89F GLN* 3.1 6.6 + - - +
90F VAL* 3.0 30.6 + - - +
131F ALA* 4.1 4.0 - - - +
138F VAL* 3.7 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ILE* 3.4 38.2 - - + +
69F ILE* 3.9 19.5 - - + +
70F ALA* 4.2 3.1 - - + +
73F LEU* 4.2 1.6 - - - +
83F ALA 2.9 17.8 + - - +
84F ASP 4.0 1.1 - - - +
86F GLY* 1.3 72.8 - - - +
88F ARG* 1.3 66.8 + - - +
90F VAL* 3.0 21.5 + - - +
91F VAL* 3.3 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ILE* 4.6 12.8 - - + -
84F ASP* 3.0 43.7 + - - +
85F ALA* 3.6 8.7 - - - +
86F GLY 3.2 0.2 - - - -
87F ALA* 1.3 76.5 - - - +
89F GLN* 1.3 62.4 + - + +
91F VAL* 3.4 10.6 - - + +
92F LEU* 2.9 35.6 + - + +
102F LEU* 4.1 12.0 - - + +
105F GLU* 3.3 19.2 + - - -
111F PRO* 3.2 36.6 - - - +
147F PRO* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F ALA* 2.9 25.4 + - + +
86F GLY* 3.1 10.3 + - - +
88F ARG* 1.3 77.4 - - - +
90F VAL* 1.3 63.6 + - - +
92F LEU* 4.1 7.8 - - - +
93F SER* 2.9 28.9 + - - -
138F VAL* 4.3 16.8 - - + +
141F GLU* 4.3 10.8 + - - +
142F ALA* 5.4 0.4 - - - +
147F PRO* 3.2 39.0 - - - +
148F LYS 2.7 26.8 + - - +
149F GLY* 3.9 1.0 - - - -
150F ILE* 3.8 9.8 + - + +
151F LEU* 3.3 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ILE* 5.9 0.4 - - + -
69F ILE* 3.9 27.6 - - + -
86F GLY 3.0 15.2 + - - +
87F ALA* 3.0 13.4 + - - +
89F GLN* 1.3 76.8 - - - +
91F VAL* 1.3 61.0 + - + +
93F SER* 3.1 6.7 + - - -
94F VAL* 3.1 25.6 - - - +
127F LEU* 4.4 24.5 - - + +
131F ALA* 3.5 25.8 - - + +
151F LEU* 4.4 5.4 - - + -
156F ILE* 3.9 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ILE* 4.0 20.4 - - + -
66F ILE* 3.7 39.9 - - + -
69F ILE* 5.7 1.1 - - + -
87F ALA 3.3 5.1 + - - +
88F ARG* 3.4 11.4 - - - +
90F VAL* 1.3 81.5 - - + +
92F LEU* 1.3 66.1 + - + +
93F SER 3.4 0.2 - - - -
94F VAL* 3.9 6.9 + - - +
99F GLY* 3.9 0.3 - - - -
100F ILE* 3.1 43.4 + - + +
102F LEU* 4.3 16.2 - - + -
113F THR* 4.5 5.2 - - + -
117F PHE* 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F ARG* 2.9 23.1 + - + +
89F GLN* 3.9 17.7 - - - +
90F VAL 3.3 0.2 - - - -
91F VAL* 1.3 81.1 - - + +
93F SER* 1.3 60.1 + - - +
94F VAL 3.3 1.3 + - - -
98F SER* 2.8 34.5 - - - +
99F GLY* 4.0 17.5 - - - +
100F ILE 5.3 2.9 - - - +
102F LEU* 6.1 4.9 - - + -
147F PRO* 3.1 35.4 - - + +
148F LYS* 4.5 2.0 - - - -
149F GLY* 3.9 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F GLN 2.9 17.8 + - - -
90F VAL 3.1 10.4 + - - -
91F VAL 3.4 0.2 - - - -
92F LEU* 1.3 76.9 - - - +
94F VAL* 1.3 56.1 + - - +
98F SER 5.3 0.2 - - - -
149F GLY* 3.5 22.1 - - - +
151F LEU* 3.6 26.1 - - - +
152F PRO 5.3 0.2 - - - -
153F ALA* 3.7 20.1 - - - +
156F ILE* 3.1 18.5 - - - +
----------------------------------------------------------
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