Contacts of the helix formed by residues 75 - 90 (chain L) 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 HIS 75 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L VAL* 1.3 73.1 - - + +
76L ALA* 1.3 60.2 + - - +
77L VAL 3.4 0.4 + - - -
78L GLU* 3.5 7.7 + - + +
79L ARG* 3.0 73.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L VAL* 3.2 15.4 - - + +
75L HIS* 1.3 78.8 - - - +
77L VAL* 1.3 58.8 + - + +
79L ARG* 4.3 5.1 - - - +
80L ALA* 2.9 29.2 + - - +
169L LEU* 3.4 35.0 - - + +
173L HIS* 5.3 0.2 + - - -
199L LEU 4.2 2.5 - - - +
200L ALA* 4.5 6.3 - - - +
203L GLY* 3.7 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L ILE* 4.7 14.1 - - + -
56L PRO* 4.4 15.7 - - + +
74L VAL* 3.6 16.4 + - + +
75L HIS 3.4 0.6 - - - -
76L ALA* 1.3 74.8 - - + +
78L GLU* 1.3 69.7 + - - +
80L ALA* 3.1 7.4 + - - +
81L PHE* 2.9 54.9 + - + -
200L ALA* 3.9 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55L VAL* 4.3 31.8 - - + +
56L PRO* 4.8 9.2 - - - +
74L VAL 2.5 26.1 + - - +
75L HIS* 3.5 9.2 + - + +
76L ALA 3.4 0.2 - - - -
77L VAL* 1.3 78.9 - - - +
79L ARG* 1.3 66.7 + - - +
81L PHE* 2.9 15.7 + - - +
82L TYR* 2.9 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75L HIS* 3.0 52.8 + - + +
76L ALA* 4.3 6.4 - - - +
78L GLU* 1.3 75.2 - - - +
80L ALA* 1.3 57.2 + - - +
82L TYR* 4.5 6.5 - - + +
83L ALA* 2.9 37.2 + - + +
169L LEU* 3.3 37.7 - - - +
170L ASP* 4.1 24.7 - - - +
173L HIS* 4.0 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L ALA 2.9 21.3 + - - +
77L VAL* 3.3 8.1 - - - +
78L GLU 3.1 0.4 - - - -
79L ARG* 1.3 76.8 - - - +
81L PHE* 1.3 57.0 + - + +
84L VAL* 3.2 26.5 - - - +
173L HIS* 4.2 6.8 - - + -
196L ILE* 3.8 12.2 - - + +
199L LEU* 3.6 15.3 - - + +
200L ALA* 3.5 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L ILE* 4.5 16.8 - - + -
9L HIS* 4.7 5.2 - - + -
10L ALA* 4.6 11.4 - - + -
13L LEU* 4.3 14.4 - - + +
51L VAL* 4.1 16.4 - - + -
54L TYR 3.4 20.9 - - - -
55L VAL* 3.6 14.1 - - + -
56L PRO* 3.4 33.7 - - + -
77L VAL* 2.9 31.0 + - + -
78L GLU* 2.9 8.2 + - - +
80L ALA* 1.3 77.5 - - + +
82L TYR* 1.3 60.6 + - + +
83L ALA 3.2 1.3 - - - -
84L VAL* 3.2 3.9 + - - +
85L ALA* 2.9 29.5 + - - +
196L ILE* 3.2 33.2 - - + +
200L ALA* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L MET* 3.6 25.1 - - + +
47L ALA* 3.2 42.0 - - + +
48L HIS* 3.4 26.3 + + - -
51L VAL* 3.5 24.5 - - + -
52L ALA* 3.9 21.8 - - - +
55L VAL* 5.0 6.0 - - + +
78L GLU* 2.9 47.0 + - + +
79L ARG* 4.4 5.2 - - + +
81L PHE* 1.3 77.9 - - + +
83L ALA* 1.3 63.7 + - - +
85L ALA* 3.9 5.1 - - - +
86L ALA* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L VAL 4.9 12.4 - - - -
79L ARG* 2.9 19.3 + - + +
82L TYR* 1.3 76.9 - - - +
84L VAL* 1.3 62.4 + - + +
86L ALA* 3.4 4.8 + - - +
87L ILE* 2.9 28.9 + - - +
173L HIS* 3.4 26.9 - - + +
176L LEU* 6.3 0.9 - - + -
177L PRO* 6.5 1.1 - - + -
199L LEU* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L ALA 3.2 20.6 - - - +
81L PHE 3.2 2.5 + - - +
83L ALA* 1.3 74.4 - - - +
85L ALA* 1.3 62.8 + - - +
87L ILE* 3.1 8.5 - - + +
88L MET* 2.9 29.7 + - + +
176L LEU* 5.5 1.3 - - + -
192L TRP* 3.5 34.1 - - + +
195L LEU* 4.7 7.0 - - + -
196L ILE* 3.4 36.8 - - + +
199L LEU* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L LEU* 4.8 7.9 - - + -
17L VAL* 4.3 23.6 - - + +
31L LEU* 4.3 7.3 - - + +
51L VAL* 3.9 28.5 - - + -
81L PHE 2.9 17.4 + - - +
82L TYR 4.0 2.5 - - - +
84L VAL* 1.3 78.0 - - - +
86L ALA* 1.3 60.2 + - - +
88L MET* 3.4 6.8 + - - +
89L ALA* 3.0 23.7 + - - +
196L ILE* 5.5 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L LEU* 3.3 29.1 - - + +
32L ARG* 4.4 1.4 - - - -
34L GLY* 4.4 1.8 - - - -
35L VAL* 3.4 30.7 - - - +
82L TYR 3.0 19.1 + - - +
83L ALA 3.9 2.2 - - - +
85L ALA* 1.3 75.0 - - - +
87L ILE* 1.3 65.5 + - - +
89L ALA* 3.1 5.9 + - - +
90L ALA* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L VAL* 5.0 7.7 - - + +
83L ALA 2.9 12.4 + - - +
84L VAL* 3.1 26.5 - - + +
86L ALA* 1.3 76.3 - - - +
88L MET* 1.3 68.2 + - - +
90L ALA* 3.0 17.0 + - + +
91L GLN* 3.7 6.6 + - - +
176L LEU* 6.2 3.8 - - + -
177L PRO* 3.5 34.3 - - + -
180L VAL* 4.0 21.8 - - + -
181L LEU* 3.5 35.9 - - + +
192L TRP* 3.5 22.8 - - + -
195L LEU* 5.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 88 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L VAL* 4.0 17.0 - - + +
17L VAL* 3.4 32.8 - - + -
18L SER* 4.3 13.2 - - - -
21L ILE* 4.0 14.7 - - + +
84L VAL* 2.9 20.9 + - + +
85L ALA* 3.8 6.1 - - - +
87L ILE* 1.3 78.6 - - - +
89L ALA* 1.3 61.4 + - - +
91L GLN* 3.2 45.6 + - - +
96L ARG* 4.7 0.2 - - - +
192L TRP* 3.3 48.5 - - + -
196L ILE* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L ILE* 4.0 16.5 - - + +
28L ARG* 3.6 41.6 + - + +
31L LEU* 3.7 25.8 - - + -
32L ARG* 3.9 7.6 - - - +
85L ALA 3.0 17.5 + - - +
86L ALA 3.1 6.2 + - - +
88L MET* 1.3 78.9 - - - +
90L ALA* 1.3 57.4 + - - +
91L GLN 3.4 1.2 + - - +
96L ARG* 4.6 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L ARG* 3.5 30.5 - - + +
35L VAL* 5.2 8.3 - - + -
86L ALA 3.0 11.7 + - - +
87L ILE* 3.0 11.1 + - + +
89L ALA* 1.3 76.8 - - - +
91L GLN* 1.3 65.1 + - - +
92L PRO* 3.7 1.4 - - - +
181L LEU* 3.5 28.8 - - + +
----------------------------------------------------------
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