Contacts of the helix formed by residues 90 - 102 (chain A) in PDB entry 4YET
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 THR 90 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU 3.8 9.0 - - - +
89A PRO* 1.3 81.0 - - - +
91A GLY* 1.3 68.5 + - - +
93A ILE* 3.2 10.9 - - - +
94A ARG* 4.0 3.8 - - - +
185A TRP* 3.8 18.9 - - + +
186A ASP* 4.4 8.5 + - - -
189A ASN* 3.0 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 1.3 76.9 - - - +
92A PRO* 1.3 75.3 - - - +
94A ARG* 3.0 20.9 + - - +
95A LYS* 3.6 3.5 + - - +
189A ASN* 3.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY* 1.3 84.0 - - - +
93A ILE* 1.3 60.1 + - - +
95A LYS* 3.1 12.2 + - + +
96A LYS* 3.1 25.9 + - + +
189A ASN* 3.4 20.0 - - + +
192A LEU* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 4.3 3.1 - - + -
90A THR 3.2 15.0 - - - +
92A PRO* 1.3 71.3 - - - +
94A ARG* 1.3 64.4 + - - +
96A LYS* 4.4 7.6 - - + +
97A ILE* 2.9 55.4 + - + +
126A LEU* 3.9 9.0 - - + -
134A ALA* 5.0 0.7 - - + -
154A LEU* 3.7 30.1 - - + -
185A TRP* 3.8 26.9 - - + +
188A ALA* 4.0 18.2 - - + -
189A ASN* 2.8 23.9 + - - +
192A LEU* 3.8 13.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
89A PRO* 3.5 47.9 + - + +
90A THR* 4.0 3.6 - - - +
91A GLY 3.0 13.9 + - - +
93A ILE* 1.3 82.6 - - - +
95A LYS* 1.3 63.8 + - - +
97A ILE* 3.3 1.7 + - - +
98A GLU* 2.9 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY 3.6 2.7 + - - +
92A PRO* 3.1 16.0 + - + +
94A ARG* 1.3 82.6 - - - +
96A LYS* 1.3 59.2 + - + +
98A GLU* 3.3 5.5 + - - +
99A GLU* 3.0 59.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO* 3.1 15.2 + - - +
93A ILE* 3.9 10.1 - - + +
95A LYS* 1.3 77.8 - - + +
97A ILE* 1.3 63.9 + - - +
99A GLU* 3.4 18.8 + - - +
100A LYS* 3.0 25.8 + - - +
128A LEU* 3.9 20.6 - - + -
132A GLY* 2.9 30.7 + - - +
133A THR* 5.0 0.4 - - - -
134A ALA* 4.1 20.7 + - + +
154A LEU* 5.9 0.2 - - + -
192A LEU* 4.1 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 4.6 10.1 - - + -
93A ILE* 2.9 48.6 + - + +
94A ARG* 3.7 5.4 - - - +
96A LYS* 1.3 78.0 - - - +
98A GLU* 1.3 63.4 + - + +
101A PHE* 2.9 36.3 + - + +
103A SER 4.3 0.9 - - - +
104A PHE* 4.2 17.3 - - - +
107A PHE* 4.0 44.2 - - + -
126A LEU* 4.0 22.0 - - + -
134A ALA* 4.2 4.9 - - + -
185A TRP* 5.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 5.8 0.8 - - + +
94A ARG* 2.9 59.8 + - + +
95A LYS* 3.9 5.7 - - - +
97A ILE* 1.3 81.8 - - + +
99A GLU* 1.3 59.3 + - + +
102A GLY* 2.9 43.9 + - - +
103A SER* 4.4 7.2 - - - +
104A PHE* 4.8 4.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LYS* 3.0 52.5 + - + +
96A LYS* 3.7 24.4 + - - +
97A ILE 3.2 0.2 - - - -
98A GLU* 1.3 79.4 - - + +
100A LYS* 1.3 62.6 + - - +
102A GLY* 4.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LYS 3.0 17.2 + - - +
99A GLU* 1.3 79.3 - - - +
101A PHE* 1.3 88.3 + - + +
102A GLY 3.6 0.4 + - - -
129A LYS* 4.6 9.3 - - - +
133A THR* 5.3 8.3 + - - -
134A ALA* 3.3 30.5 + - + +
135A ASP* 3.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 2.9 24.7 + - + +
100A LYS* 1.3 100.7 - - + +
102A GLY* 1.3 57.6 + - - +
103A SER 3.1 8.5 + - - +
106A ALA* 3.2 17.9 - - + +
107A PHE* 3.4 55.4 - + + +
110A ASP* 3.5 23.8 - - + -
126A LEU* 4.8 0.9 - - + -
134A ALA* 4.7 12.8 - - + -
135A ASP* 4.4 8.7 - - - -
136A ILE* 4.0 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 2.9 30.4 + - - +
99A GLU 4.4 1.0 + - - -
100A LYS 3.6 1.4 - - - -
101A PHE* 1.3 74.6 - - - +
103A SER* 1.3 60.5 + - - +
----------------------------------------------------------
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