Contacts of the helix formed by residues 88 - 99 (chain A) in PDB entry 1H5Y
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 SER 88 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.4 8.3 + - - +
87A ARG* 1.3 83.6 + - - +
89A LEU* 1.3 65.8 + - - +
90A GLU* 3.3 9.7 + - - +
91A ASP* 3.2 24.1 + - - +
92A ALA* 3.1 18.2 + - - +
108A ALA* 4.4 0.4 - - - +
115A LEU* 4.2 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 1.3 75.0 - - - +
90A GLU* 1.3 63.2 + - + +
92A ALA* 3.3 4.7 + - - +
93A THR* 2.8 40.9 + - - +
115A LEU* 3.6 22.1 - - + +
118A LEU* 4.4 30.3 - - + +
119A LEU* 3.8 25.1 - - + +
122A GLU* 5.4 3.8 - - + -
123A PHE* 4.7 6.5 - - + -
2B HIS* 3.6 45.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 3.1 8.6 + - - +
89A LEU* 1.3 82.5 - - + +
91A ASP* 1.3 66.4 + - - +
93A THR* 3.2 16.2 + - - +
94A THR* 2.9 27.6 + - - -
2B HIS* 5.4 12.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.7 13.6 + - - +
85A GLY 3.5 6.5 - - - +
86A VAL* 3.9 14.6 - - + -
87A ARG* 2.8 61.7 + - - +
88A SER* 3.2 17.9 + - - +
90A GLU* 1.3 73.7 - - - +
92A ALA* 1.3 66.7 + - - +
94A THR* 3.2 9.0 + - - -
95A LEU* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.7 11.6 - - + +
88A SER 3.1 9.5 + - - +
89A LEU 3.6 6.3 - - - +
91A ASP* 1.3 79.8 - - - +
93A THR* 1.3 63.6 + - - +
95A LEU* 3.1 6.1 + - - +
96A PHE* 3.0 30.0 + - + -
103A VAL* 4.0 20.9 - - + +
119A LEU* 3.5 32.8 - - + -
123A PHE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 2.8 28.9 + - - +
90A GLU* 3.5 19.7 + - - +
91A ASP 3.2 0.2 - - - -
92A ALA* 1.3 78.3 - - - +
94A THR* 1.3 57.5 + - - +
96A PHE* 3.3 3.1 + - - +
97A ARG* 2.9 28.5 + - + +
122A GLU* 5.3 4.7 + - - +
123A PHE* 3.7 31.3 - - + -
2B HIS* 5.9 2.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 3.7 35.4 - - + -
90A GLU 2.9 14.6 + - - -
91A ASP* 3.4 11.3 - - - -
93A THR* 1.3 78.0 - - - +
95A LEU* 1.3 57.8 + - - +
97A ARG* 3.2 8.8 + - + +
98A ALA* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.1 11.7 - - - +
65A PHE* 4.1 11.7 - - + -
66A ILE* 4.1 25.8 - - + -
69A VAL* 4.5 9.7 - - + +
82A VAL* 4.0 27.8 - - + +
83A GLY* 5.2 0.2 - - - -
86A VAL* 3.6 30.5 - - + -
91A ASP 3.2 13.0 + - - +
92A ALA* 3.1 6.6 + - - +
94A THR* 1.3 73.4 - - - +
96A PHE* 1.3 68.0 + - - +
98A ALA* 3.2 5.5 + - - +
99A GLY 3.2 6.1 + - - -
100A ALA* 3.0 26.2 + - + +
103A VAL* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA* 3.0 20.6 + - + -
93A THR 3.6 6.5 - - - +
95A LEU* 1.3 76.2 - - - +
97A ARG* 1.3 63.8 + - - +
99A GLY* 3.0 14.9 + - - -
100A ALA 3.5 18.0 + - - +
101A ASP 3.7 22.2 - - - -
103A VAL* 3.7 29.4 - - + -
119A LEU* 4.7 10.3 - - + -
123A PHE* 3.4 58.3 - + + -
127A SER* 3.3 34.3 - - - -
128A THR* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 2.9 15.8 + - + +
94A THR* 3.5 12.6 - - + +
96A PHE* 1.3 78.5 - - - +
98A ALA* 1.3 59.4 + - - +
99A GLY* 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 4.0 33.0 - - + +
69A VAL* 4.3 10.1 - - + -
70A LYS* 3.4 39.9 + - + +
73A ALA* 4.1 2.9 - - - +
74A GLU* 6.0 0.2 - - - +
94A THR 2.9 15.2 + - - +
95A LEU* 3.2 7.8 + - - +
97A ARG* 1.3 76.7 - - - +
99A GLY* 1.3 56.7 + - - +
100A ALA 3.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 3.7 23.5 - - - +
80A VAL* 4.6 0.9 - - - +
96A PHE 3.0 9.6 + - - -
97A ARG 3.1 2.1 - - - -
98A ALA* 1.3 81.3 - - - +
100A ALA* 1.3 67.6 + - - +
101A ASP* 3.4 12.1 + - - +
----------------------------------------------------------
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