Contacts of the helix formed by residues 102 - 111 (chain A) in PDB entry 4U86
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 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 4.3 2.5 - - - -
99A GLY* 5.2 3.5 - - - +
101A GLU* 1.3 81.8 + - - +
103A PHE* 1.3 67.1 + - - +
104A GLU* 3.8 16.2 - - + +
105A SER* 3.2 13.5 + - - +
106A LEU* 3.0 23.4 + - - +
119A ARG* 5.7 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 3.6 24.2 - - - -
59A HIS* 3.6 29.6 - - - -
60A LEU* 3.9 7.6 - - + -
96A ILE* 3.9 41.7 - - + +
101A GLU 4.1 0.2 + - - -
102A ASP* 1.3 72.0 - - - +
104A GLU* 1.3 72.1 + - + +
106A LEU* 3.3 2.8 + - - +
107A ALA* 2.8 32.1 + - + +
119A ARG 4.0 10.3 - - - -
146A MET* 4.2 12.6 - - - -
158A ILE* 3.8 26.7 - - + -
160A LEU* 4.1 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER* 6.1 0.2 - - - +
102A ASP* 3.8 11.1 - - + +
103A PHE* 1.3 97.8 + - + +
105A SER* 1.3 57.9 + - - +
107A ALA* 3.4 1.9 + - - +
108A SER* 2.9 34.5 + - - -
119A ARG* 3.6 62.9 + - + +
160A LEU* 4.8 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU* 3.5 16.7 + - - -
102A ASP* 3.2 20.4 + - - +
104A GLU* 1.3 77.5 - - - +
106A LEU* 1.3 65.1 + - - +
108A SER* 3.3 5.8 + - - -
109A GLN* 3.0 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.7 14.4 - - + +
92A TYR* 3.8 29.6 - - + +
95A LYS* 4.5 7.0 - - + -
96A ILE* 3.6 30.1 - - + -
101A GLU* 3.9 36.3 - - + +
102A ASP 3.0 15.3 + - - +
103A PHE* 3.8 2.5 - - - +
105A SER* 1.3 75.1 - - - +
107A ALA* 1.3 59.5 + - - +
109A GLN* 4.6 1.8 - - - +
110A PHE* 2.8 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS 3.8 20.2 - - - +
60A LEU* 3.7 15.8 - - + +
103A PHE* 2.8 27.8 + - + +
104A GLU 3.8 4.0 - - - +
105A SER 3.3 0.2 - - - -
106A LEU* 1.3 73.1 - - - +
108A SER* 1.4 63.2 + - - +
111A SER* 3.1 27.4 + - - -
116A ALA* 3.3 7.3 - - - +
119A ARG 3.8 20.6 - - - +
120A GLY* 4.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TRP* 3.6 18.9 - - - -
104A GLU 2.9 19.1 + - - -
105A SER* 3.7 6.7 - - - -
106A LEU 3.2 0.2 - - - -
107A ALA* 1.4 77.4 - - - +
109A GLN* 1.3 63.2 + - - +
116A ALA* 3.3 18.8 + - - +
117A LYS* 4.9 2.4 + - - +
119A ARG* 3.4 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TRP* 3.7 11.8 - - - -
74A ARG* 3.3 17.2 + - - -
101A GLU* 4.6 5.0 + - - +
105A SER* 3.0 36.2 + - - +
106A LEU* 4.3 4.0 + - - +
108A SER* 1.3 82.6 - - - +
110A PHE* 1.3 96.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.4 5.4 - - + +
61A LEU 3.8 5.0 - - - +
62A VAL* 4.7 4.0 - - - +
74A ARG* 3.5 38.3 + - - +
92A TYR* 3.3 46.2 - + + +
106A LEU* 2.8 43.3 + - + +
109A GLN* 1.3 111.4 - - + +
111A SER* 1.3 61.5 + - - +
112A ASP* 3.4 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 4.0 8.1 + - - -
60A LEU* 3.7 12.8 - - - +
61A LEU* 3.0 33.3 + - - +
73A TRP* 2.8 32.9 + - - -
74A ARG* 4.0 1.0 - - - -
106A LEU 4.0 1.4 + - - -
107A ALA* 3.1 21.4 + - - -
110A PHE* 1.3 75.1 - - - +
112A ASP* 1.3 53.1 + - - +
113A OCS 3.0 13.5 + - - +
115A SER* 4.7 1.8 + - - -
116A ALA* 3.7 9.7 - - - +
----------------------------------------------------------
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