Contacts of the helix formed by residues 85 - 97 (chain A) in PDB entry 4O5A
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 ILE 85 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.3 0.9 - - + -
72A LEU* 3.9 26.0 - - + -
84A TYR* 1.3 99.8 - - + +
86A MSE 1.3 60.5 + - - +
88A LEU* 3.2 5.7 + - + +
89A ILE* 2.9 49.1 + - + +
133A LEU* 3.7 30.1 - - + -
134A ASN* 5.4 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR 3.2 4.2 - - - +
85A ILE* 1.3 80.6 - - - +
87A ARG* 1.3 62.4 + - + +
89A ILE* 3.3 26.1 + - + +
90A SER* 3.0 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.1 18.9 + - - +
86A MSE 1.3 78.9 - - + +
88A LEU* 1.3 63.1 + - - +
90A SER* 3.3 5.8 + - - -
91A GLY* 3.0 18.7 + - - -
283A ASP* 3.0 29.7 + - - +
284A SER* 3.4 10.1 - - - -
299A ARG 5.3 2.4 + - - -
301A ILE* 3.4 40.2 - - + +
302A LEU* 3.4 23.4 - - + +
403A GOL 3.3 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.9 0.9 - - + -
84A TYR* 3.0 30.5 + - + +
85A ILE* 3.2 12.3 + - + +
87A ARG* 1.3 77.6 - - - +
89A ILE* 1.3 58.7 + - + +
91A GLY* 3.2 2.4 + - - -
92A LEU* 2.8 39.0 + - + +
131A LEU* 4.5 10.8 - - + -
133A LEU* 3.9 39.7 - - + -
156A LEU* 4.0 19.7 - - + -
301A ILE* 3.5 15.4 - - + +
304A SER* 4.3 4.0 - - - -
305A GLY* 3.6 27.8 - - - +
308A ALA* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.5 12.3 - - + -
72A LEU* 4.6 10.1 - - + -
85A ILE* 2.9 39.2 + - + +
86A MSE 3.7 24.9 - - + +
87A ARG 3.3 0.2 - - - -
88A LEU* 1.3 78.4 - - + +
90A SER* 1.3 56.8 + - - +
92A LEU* 3.4 9.3 + - + +
93A GLY* 2.9 26.7 + - - -
103A LEU* 4.0 30.1 - - + -
105A VAL* 5.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A MSE 3.0 22.4 + - - +
87A ARG* 3.6 10.0 - - - -
88A LEU 3.3 0.2 - - - -
89A ILE* 1.3 77.9 - - - +
91A GLY* 1.3 61.3 + - - +
93A GLY* 3.4 1.7 + - - -
94A SER* 3.0 22.7 + - - -
302A LEU* 3.8 13.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
87A ARG 3.0 12.9 + - - -
88A LEU 3.7 2.5 - - - -
90A SER* 1.3 73.1 - - - +
92A LEU* 1.3 68.2 + - - +
94A SER* 2.9 24.5 + - - -
95A ALA 3.5 0.7 + - - -
302A LEU* 3.3 30.4 - - - +
306A ARG* 3.3 17.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.9 1.8 - - + -
88A LEU* 2.8 31.9 + - + +
89A ILE* 3.6 16.4 - - + +
91A GLY* 1.3 70.3 - - - +
93A GLY* 1.3 59.2 + - - +
95A ALA 3.0 4.2 + - - -
96A LEU* 2.9 40.5 + - + +
103A LEU* 4.3 20.2 - - + -
131A LEU* 3.7 25.6 - - + -
305A GLY* 3.4 23.1 - - - +
308A ALA* 4.1 4.5 - - + -
309A ALA* 3.6 13.8 - - + +
312A MSE 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE 2.9 17.5 + - - -
90A SER 3.8 2.0 - - - -
91A GLY 3.3 0.2 - - - -
92A LEU* 1.3 76.0 - - - +
94A SER* 1.3 62.1 + - - +
96A LEU* 4.3 9.6 - - - +
97A GLU* 2.9 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 3.0 14.9 + - - -
91A GLY* 2.9 18.4 + - - -
93A GLY* 1.3 76.0 - - - +
95A ALA* 1.3 57.2 + - - +
97A GLU* 4.5 4.3 - - - +
98A GLU* 3.3 15.6 + - - +
306A ARG* 3.2 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY 3.5 1.1 + - - +
92A LEU 3.0 2.2 + - - +
94A SER* 1.3 79.8 + - - +
96A LEU* 1.3 67.1 + - - +
97A GLU 3.2 1.8 - - - -
98A GLU* 3.2 22.9 + - - +
99A ARG* 3.9 2.6 + - - +
306A ARG* 3.7 28.7 - - + +
309A ALA* 3.7 23.1 - - + -
310A GLN* 4.0 15.9 - - + +
313A LEU* 4.3 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.7 35.4 - - + -
92A LEU* 2.9 36.0 + - + +
93A GLY* 4.2 6.7 - - - +
95A ALA* 1.3 75.9 - - - +
97A GLU* 1.3 62.3 + - - +
99A ARG* 3.1 8.3 + - - +
101A TYR* 2.9 47.6 + - + +
102A SER* 4.3 15.7 - - - +
103A LEU* 4.4 13.7 - - + +
309A ALA* 3.8 19.1 - - + -
313A LEU* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY* 2.9 28.4 + - - +
94A SER* 4.5 4.9 - - - +
96A LEU* 1.3 76.5 - - - +
98A GLU* 1.3 63.0 + - + +
99A ARG 3.1 0.9 + - - -
100A ASP* 3.2 24.4 + - - +
101A TYR 4.2 11.8 - - - +
102A SER* 5.9 0.2 - - - -
----------------------------------------------------------
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