Contacts of the helix formed by residues 93 - 103 (chain H) in PDB entry 2EHO
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 GLN 93 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H GLU* 3.9 16.0 + - - +
88H LEU* 3.0 34.6 - - + +
89H PRO 3.6 7.4 - - - +
90H LYS* 2.7 33.9 + - - +
92H TYR* 1.3 74.9 - - - +
94H GLU* 1.3 67.6 + - - +
95H GLY 3.3 2.9 - - - +
96H TRP* 3.0 15.5 + - - +
97H ARG* 3.0 13.6 + - - +
130H GLU* 5.4 2.5 - - - +
40K LEU* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H GLN* 1.3 72.3 - - - +
95H GLY* 1.3 58.2 + - - +
97H ARG* 3.1 32.1 + - + +
98H THR* 2.8 40.7 + - - +
130H GLU* 5.0 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H GLN* 3.1 3.4 + - - +
94H GLU* 1.3 78.8 - - - +
96H TRP* 1.3 56.9 + - - +
98H THR* 3.4 8.7 + - - +
99H VAL* 3.1 27.5 + - - +
40K LEU* 6.1 1.3 - - - -
41K PRO* 4.0 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H LYS* 3.6 18.8 - - - +
91H ILE* 3.4 47.3 - - + +
93H GLN 3.0 5.6 + - - +
95H GLY* 1.3 71.3 - - - +
97H ARG* 1.3 58.0 + - - +
98H THR 3.0 1.6 - - - -
99H VAL* 2.9 30.7 + - + +
100H PHE* 2.7 43.0 + + + -
106H VAL* 5.7 0.2 - - + -
107H VAL* 4.1 26.9 - - + -
112H MSE 5.0 9.6 - - + +
18K ILE* 4.0 22.9 - - + -
39K GLY 3.1 22.2 + - - -
40K LEU* 4.8 1.8 - - + -
41K PRO* 3.6 19.8 - - + +
59K ARG* 4.2 25.4 - - - -
61K LEU* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ILE 4.7 0.8 + - - +
92H TYR* 2.8 34.8 + - - +
93H GLN* 3.0 6.8 + - - +
94H GLU* 3.1 38.7 + - + +
96H TRP* 1.3 77.6 - - - +
98H THR* 1.3 60.2 + - - +
100H PHE* 3.9 6.3 - - + +
101H SER* 3.3 21.3 + - - -
130H GLU* 3.5 32.7 + - - +
133H ASP* 3.6 33.5 - - - +
134H ILE* 3.9 20.8 - - - +
137H SER* 3.1 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H GLU* 2.8 21.0 + - - +
95H GLY* 3.4 12.7 - - - +
97H ARG* 1.3 77.5 - - - +
99H VAL* 1.3 70.0 + - + +
101H SER* 3.3 8.6 + - - -
102H ALA* 3.3 18.2 + - + +
43K GLU* 5.4 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H GLY 3.1 16.1 + - - +
96H TRP* 2.9 21.6 + - + +
98H THR* 1.3 80.1 - - + +
100H PHE* 1.3 63.9 + - - +
102H ALA* 3.0 16.9 + - + +
103H ASP* 3.1 11.9 + - + +
106H VAL* 4.5 15.5 - - + -
107H VAL* 4.7 0.7 - - + -
16K THR* 4.5 7.2 - - + +
41K PRO* 3.8 27.1 - - + -
61K LEU* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ILE* 3.8 29.4 - - + -
96H TRP* 2.7 34.7 + + + +
97H ARG* 3.9 9.2 - - + +
99H VAL* 1.3 73.8 - - - +
101H SER* 1.3 57.7 + - - +
103H ASP 4.7 0.7 - - - -
104H PRO* 3.0 43.1 - - + +
107H VAL* 3.6 29.6 - - + -
109H LEU* 3.5 32.8 - - + -
116H PHE* 3.7 25.4 - + - -
137H SER* 4.5 6.5 - - - +
140H GLN* 5.7 1.3 - - - +
141H THR* 3.9 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H ARG 3.3 12.7 + - - -
98H THR* 3.5 12.1 - - - -
99H VAL 3.1 0.6 - - - -
100H PHE* 1.3 81.8 - - - +
102H ALA* 1.3 61.0 + - - +
104H PRO* 4.5 3.5 - - - +
140H GLN* 3.7 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H THR* 3.3 8.2 + - + +
99H VAL* 3.0 9.4 + - - +
101H SER* 1.3 81.8 + - - +
103H ASP* 1.3 63.5 + - + +
104H PRO* 4.1 1.6 - - - +
64K GLU* 3.9 18.2 - - + +
70K LYS* 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H VAL* 3.1 10.2 + - + +
100H PHE 3.8 0.9 - - - -
102H ALA* 1.3 84.4 - - + +
104H PRO* 1.3 63.2 - - - +
105H ASN* 3.5 22.7 + - - +
106H VAL* 2.9 49.7 + - + +
107H VAL* 4.6 0.3 - - - +
62K PRO* 4.7 2.8 - - - +
63K PRO 4.8 0.9 - - - +
64K GLU* 3.7 33.6 + - + +
70K LYS* 4.3 10.1 + - - +
----------------------------------------------------------
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