Contacts of the helix formed by residues 90 - 102 (chain D) in PDB entry 2HYF
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 90 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ASN* 2.8 42.9 + - - +
112C ARG* 4.9 2.8 + - - -
88D GLY 3.8 2.6 + - - +
89D VAL* 1.3 70.8 - - - +
91D GLU* 1.3 69.0 + - - +
92D GLU* 3.6 22.5 - - - +
93D LYS* 2.8 30.2 + - + +
94D ILE 3.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ARG* 2.6 56.1 + - - +
89D VAL 3.1 4.7 + - - +
90D ASP* 1.3 70.7 - - - +
92D GLU* 1.3 59.5 + - - +
93D LYS 2.8 6.8 + - - -
94D ILE* 3.1 24.9 + - - +
95D TYR* 4.3 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ASP* 3.6 17.1 - - - +
91D GLU* 1.3 76.5 + - - +
93D LYS* 1.3 92.0 + - + +
95D TYR* 5.1 3.2 + - - +
96D ASN* 4.0 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 4.4 13.5 - - - -
106C SER* 3.9 15.5 - - - +
108C ASN* 3.5 28.5 - - + +
150C SO4 2.9 35.4 - - - +
89D VAL* 4.2 4.9 - - + -
90D ASP* 2.8 23.4 + - - +
91D GLU 2.8 1.6 + - - -
92D GLU* 1.3 115.5 + - + +
94D ILE* 1.3 62.1 + - - +
95D TYR 3.3 2.7 - - - -
96D ASN* 3.3 8.2 + - - +
97D ASP* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D GLU* 3.5 43.5 - - + +
84D LEU* 3.3 27.1 - - + -
85D ARG* 3.9 13.5 - - - +
89D VAL* 3.3 31.4 - - + +
90D ASP 3.8 4.7 - - - +
91D GLU* 3.1 32.6 + - - +
93D LYS* 1.3 77.1 - - - +
95D TYR* 1.3 64.4 + - - +
97D ASP* 4.4 2.9 - - - -
98D VAL* 2.9 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLN* 4.4 12.5 + - - -
15D MSE 6.0 3.3 - - - -
31D ALA* 4.5 11.2 + - - +
32D LEU* 6.1 0.3 - - - +
77D HIS* 3.8 14.8 - + - -
81D GLU* 4.0 16.6 - - - +
91D GLU 4.3 3.4 + - - +
92D GLU 5.1 2.4 + - - +
93D LYS 3.3 0.6 - - - -
94D ILE* 1.3 80.0 - - - +
96D ASN* 1.3 71.7 + - - +
98D VAL* 3.9 2.1 - - - +
99D GLU* 2.8 72.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C HIS 4.6 1.5 - - - +
92D GLU 4.0 16.6 + - - -
93D LYS* 3.3 7.2 + - - +
95D TYR* 1.3 85.5 - - - +
97D ASP* 1.3 59.8 + - - +
99D GLU* 3.6 4.2 - - - +
100D GLY* 2.7 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C HIS 3.9 6.5 - - - +
105C LEU* 3.6 9.0 - - + -
106C SER* 2.6 42.1 + - - -
109C SER* 2.4 28.8 + - - -
84D LEU* 3.6 18.8 - - + -
89D VAL* 4.0 5.7 - - - +
93D LYS 3.0 19.9 + - - +
96D ASN* 1.3 79.2 - - - +
98D VAL* 1.3 62.9 + - - +
100D GLY 3.4 0.5 + - - -
101D ILE* 3.1 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D HIS* 3.6 45.1 - - + +
80D LEU* 3.7 16.2 - - + -
81D GLU* 3.5 34.5 - - + +
84D LEU* 3.7 12.8 - - + -
94D ILE* 2.9 21.9 + - + +
95D TYR 3.9 2.2 - - - +
97D ASP* 1.3 72.2 - - - +
99D GLU* 1.3 59.3 + - - +
100D GLY 2.9 4.0 - - - -
101D ILE* 3.0 6.5 + - - -
102D GLU* 2.8 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASP* 5.4 5.9 - - - +
11D GLU* 3.7 3.6 - - - +
12D GLN* 5.4 1.3 - - - +
32D LEU* 5.4 7.8 - - - +
77D HIS* 2.8 27.9 + - + -
95D TYR* 2.8 65.5 + - + +
96D ASN* 3.9 5.4 - - - +
98D VAL* 1.3 72.8 - - - +
100D GLY* 1.3 58.9 + - - +
101D ILE 3.4 0.2 - - - -
102D GLU* 3.0 26.8 - - - +
103D HIS* 4.9 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C HIS* 3.1 38.6 + - - +
96D ASN 2.7 17.9 + - - -
97D ASP 3.7 0.4 - - - -
99D GLU* 1.3 80.9 - - - +
101D ILE* 1.3 61.9 + - - +
103D HIS 5.2 0.4 - - - -
104D HIS* 4.0 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ILE* 3.7 33.4 - - + +
104C HIS* 3.8 13.2 - - + +
105C LEU* 4.0 22.0 - - + -
80D LEU* 4.1 18.2 - - + -
83D PHE* 5.9 3.8 - - + -
84D LEU* 4.9 9.2 - - + -
97D ASP 3.1 20.4 + - - +
98D VAL* 3.0 10.3 + - - +
100D GLY* 1.3 82.9 - - - +
102D GLU* 1.3 70.2 + - - +
103D HIS 3.0 3.4 - - - -
104D HIS* 2.7 17.1 + - - +
105D LEU* 3.5 29.8 + - + +
113D ILE* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASP* 5.5 1.4 - - - -
11D GLU* 2.9 24.5 - - - +
73D LEU 5.6 0.2 - - - -
76D ARG* 2.8 41.1 + - + +
77D HIS* 2.3 37.8 + - - +
80D LEU* 3.6 23.6 - - + -
98D VAL* 2.8 19.1 + - - +
99D GLU* 3.0 29.1 - - - +
101D ILE* 1.3 77.4 - - - +
103D HIS* 1.3 77.9 + - + +
104D HIS 3.7 0.3 + - - -
105D LEU* 4.2 5.4 + - - +
----------------------------------------------------------
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