Contacts of the helix formed by residues 85 - 101 (chain A) in PDB entry 2H0D
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 GLY 85 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL 3.5 0.2 + - - -
84A PRO* 1.3 70.3 - - - +
86A LEU* 1.3 61.4 + - - +
87A PHE 3.5 2.5 - - - -
88A LYS* 3.6 18.7 + - - +
89A ASN* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.9 20.2 - - + -
25A PHE 4.4 3.6 - - - +
26A ILE* 4.1 4.5 - - + -
79A VAL* 3.5 32.5 - - + +
80A TYR* 4.0 20.6 - - + -
83A VAL* 3.3 31.3 + - + +
84A PRO 3.1 4.8 + - - -
85A GLY* 1.3 77.0 - - - +
87A PHE* 1.3 64.0 + - - +
89A ASN* 3.2 5.2 + - - +
90A GLU* 3.0 21.3 + - - +
29B GLN* 3.5 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 3.8 54.6 + + + +
83A VAL 4.7 1.0 + - - -
86A LEU* 1.3 75.9 - - - +
88A LYS* 1.3 77.6 + - + +
89A ASN 3.2 0.2 + - - -
90A GLU* 3.3 1.8 + - - +
91A MET* 3.2 58.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLY* 3.6 18.2 + - - +
86A LEU 3.4 0.4 - - - -
87A PHE* 1.3 86.9 - - + +
89A ASN* 1.3 61.1 + - - +
91A MET* 3.6 4.9 + - - +
92A LYS* 3.1 24.5 + - - +
95A ARG* 4.8 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLY 3.0 20.5 + - - +
86A LEU* 3.4 6.1 - - - +
87A PHE 3.1 0.2 - - - -
88A LYS* 1.3 77.4 - - - +
90A GLU* 1.3 57.4 + - - +
92A LYS* 3.2 10.4 + - - +
93A ARG* 3.0 55.3 + - - +
29B GLN* 3.0 16.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
26A ILE* 3.3 41.4 - - + +
80A TYR* 4.2 6.5 - - - +
86A LEU 3.0 13.5 + - - +
87A PHE 3.3 2.2 + - - +
89A ASN* 1.3 72.5 + - - +
91A MET* 1.3 79.9 + - + +
93A ARG* 3.3 9.1 + - - +
94A ARG* 3.0 52.9 + - - +
22B TYR* 2.7 30.3 + - - -
26B ARG* 4.7 4.4 + - - -
29B GLN* 2.7 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 4.4 6.7 - - + +
87A PHE* 3.2 54.6 + - + +
88A LYS* 3.9 3.8 - - - +
90A GLU* 1.3 86.0 - - + +
92A LYS* 1.3 56.5 + - - +
94A ARG* 3.4 39.9 + - - +
95A ARG* 3.0 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS 3.1 17.8 + - - +
89A ASN* 3.5 9.9 - - - +
90A GLU 3.2 0.2 - - - -
91A MET* 1.3 75.8 - - - +
93A ARG* 1.3 55.7 + - + +
95A ARG* 3.1 24.3 + - + +
96A ASP* 2.8 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASN* 3.0 33.2 + - - +
90A GLU* 3.3 13.5 + - - +
92A LYS* 1.3 77.1 - - + +
94A ARG* 1.3 57.8 + - - +
96A ASP* 3.4 8.0 + - - +
97A PHE* 3.0 27.7 + - - +
22B TYR* 3.9 17.0 + - + +
27B THR* 3.0 41.4 + - - +
28B PRO 3.1 18.8 + - - -
29B GLN* 3.1 34.9 + - - +
30B GLU* 4.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.5 13.3 - - - +
27A ASP* 3.2 27.3 + - - -
80A TYR* 4.6 2.8 + - - -
90A GLU* 3.0 33.6 + - - +
91A MET* 3.6 35.2 - - - +
93A ARG* 1.3 74.3 - - - +
95A ARG* 1.3 63.8 + - - +
97A PHE* 3.3 1.4 + - - +
98A TYR* 3.1 52.6 + - + +
22B TYR* 3.6 37.9 - - + -
23B GLU* 5.9 2.9 + - - +
26B ARG* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 4.8 2.6 + - - +
91A MET* 3.0 40.5 + - - +
92A LYS* 3.3 26.7 - - - +
94A ARG* 1.3 75.3 - - - +
96A ASP* 1.3 68.4 + - - +
98A TYR* 3.5 7.2 + - - +
99A ALA* 3.2 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS* 2.8 55.7 + - - +
93A ARG* 3.7 8.1 - - - +
95A ARG* 1.3 77.1 - - - +
97A PHE* 1.3 59.7 + - - +
99A ALA* 3.8 5.6 + - - +
100A ALA* 3.4 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG 3.0 16.7 + - - +
94A ARG 3.7 4.0 - - - +
95A ARG 3.3 0.2 - - - -
96A ASP* 1.3 75.4 - - - +
98A TYR* 1.3 81.2 + + - +
100A ALA* 3.2 3.6 + - - +
101A HIS* 3.0 73.3 + + + +
21B LEU* 3.8 30.1 - - + -
22B TYR* 3.5 33.9 - + + -
25B GLN* 3.5 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.1 41.0 + - + +
95A ARG* 4.3 5.4 - - - +
97A PHE* 1.3 96.6 - + - +
99A ALA* 1.3 64.1 + - - +
101A HIS* 3.4 24.6 + - - +
20B SER* 5.1 5.8 + - - -
21B LEU* 6.1 1.1 - - + -
22B TYR* 3.9 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG 3.2 18.5 + - - +
96A ASP* 4.0 6.3 - - - +
98A TYR* 1.3 76.8 - - - +
100A ALA* 1.3 61.6 + - - +
101A HIS* 3.7 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASP 3.4 13.4 + - - +
97A PHE* 3.2 10.9 + - - +
99A ALA* 1.3 80.7 - - - +
101A HIS* 1.3 75.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 3.0 59.4 + + + +
98A TYR* 3.4 18.0 - - - +
99A ALA 3.4 3.3 - - - +
100A ALA* 1.3 93.2 - - + +
21B LEU* 6.1 4.9 - - + -
25B GLN* 5.8 1.3 - - - -
----------------------------------------------------------
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