Contacts of the helix formed by residues 102 - 113 (chain A) in PDB entry 3PHW
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 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.5 33.6 + - - +
101A SER* 1.3 69.2 - - - +
103A LEU* 1.3 63.6 + - - +
105A ALA* 3.6 8.3 - - - +
106A SER* 2.9 24.6 + - - -
118A ILE* 3.8 13.4 - - + +
131A ILE* 4.6 4.0 - - + -
133A PHE* 3.3 30.3 - - + -
42B ARG* 5.5 0.7 - - - +
71B LEU 4.4 5.4 - - - +
72B ARG* 3.7 1.2 - - - -
73B LEU* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 4.1 8.3 - - + -
76A GLU* 4.0 28.9 - - + +
78A GLU* 3.4 16.6 + - + +
79A ALA* 4.0 14.4 - - + +
82A VAL* 3.5 32.5 - - + -
89A TYR* 3.8 21.3 - - + -
101A SER* 3.1 11.7 + - - +
102A THR* 1.3 80.6 - - - +
104A GLU* 1.3 66.4 + - - +
106A SER* 3.3 3.4 + - - -
107A MET* 3.2 35.4 + - + +
72B ARG* 3.6 9.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
41A PHE* 3.8 17.9 - - + -
42A TYR* 3.5 21.5 - - + +
65A THR* 3.6 16.8 - - + +
89A TYR* 2.8 39.0 + - - +
93A MET* 4.2 4.1 - - + +
99A TRP 4.8 3.8 - - - +
100A GLY* 3.5 3.3 - - - -
101A SER* 2.6 47.8 + - - +
103A LEU* 1.3 77.8 - - - +
105A ALA* 1.3 54.6 + - - +
107A MET* 3.0 9.2 + - - +
108A LEU* 2.7 37.8 + - - +
72B ARG* 5.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.7 16.3 - - + -
101A SER 3.0 13.7 + - - +
102A THR* 3.6 12.1 - - - +
103A LEU 3.2 0.2 - - - -
104A GLU* 1.3 76.0 - - - +
106A SER* 1.3 61.9 + - - +
108A LEU* 4.6 0.2 - - - -
109A ALA* 2.9 26.3 + - - +
116A ILE* 3.5 18.8 - - + +
118A ILE* 4.1 9.4 - - + -
133A PHE* 3.9 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN* 3.4 15.1 + - - +
76A GLU* 2.8 28.3 + - - -
78A GLU* 5.9 1.3 - - - -
102A THR 2.9 17.2 + - - -
103A LEU* 3.5 6.3 - - - -
104A GLU 3.2 0.2 - - - -
105A ALA* 1.3 78.1 - - - +
107A MET* 1.3 62.4 + - - +
109A ALA* 3.5 8.8 + - - +
110A LYS* 3.5 24.4 + - - +
133A PHE* 3.7 23.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 4.4 7.9 - - + +
68A ALA* 3.6 16.8 - - + +
69A ALA* 3.7 29.6 - - + +
72A TYR* 4.0 8.0 - - + -
73A TYR* 3.9 12.6 - - + -
76A GLU* 3.5 37.0 - - + +
89A TYR* 3.2 33.7 - - + +
103A LEU* 3.2 24.6 + - + +
104A GLU* 3.0 9.4 + - - +
106A SER* 1.3 73.2 - - - +
108A LEU* 1.3 64.5 + - + +
110A LYS* 3.3 5.4 + - - +
111A GLU* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.2 20.2 - - + -
45A ILE* 4.5 11.2 - - + -
61A ILE* 3.5 22.2 - - + +
64A LEU* 3.8 18.6 - - + +
65A THR* 3.4 46.9 - - - +
104A GLU 2.7 21.8 + - - +
105A ALA 4.0 2.7 - - - +
107A MET* 1.3 70.0 - - - +
109A ALA* 1.3 59.8 + - - +
111A GLU* 4.2 2.7 - - + -
112A MET* 2.7 53.1 + - + +
114A ILE* 4.8 0.2 - - - -
116A ILE* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 2.9 17.6 + - - +
106A SER 3.7 6.5 - - - +
107A MET 3.3 0.4 - - - -
108A LEU* 1.3 75.5 - - - +
110A LYS* 1.3 59.4 + - + +
113A GLY* 3.0 6.8 + - - -
114A ILE* 2.9 48.0 + - - +
116A ILE* 3.9 6.2 - - + +
133A PHE* 3.3 33.0 - - + +
134A GLY* 4.6 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 5.5 4.4 + - - -
15A GLY* 6.1 2.0 - - - -
72A TYR* 3.8 42.4 + - + +
76A GLU* 3.0 31.0 + - - -
106A SER* 3.5 20.9 + - - +
107A MET 3.3 5.0 + - - +
108A LEU 3.1 0.4 - - - -
109A ALA* 1.3 77.4 - - + +
111A GLU* 1.3 65.9 + - - +
113A GLY* 3.3 10.8 + - - -
135C ASP* 5.7 12.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.5 32.9 - - + +
67A SER* 2.6 29.8 + - - -
68A ALA* 3.4 25.6 - - + -
71A LYS* 2.5 33.7 + - - -
72A TYR* 3.8 8.8 - - + -
107A MET 3.0 8.3 + - - +
108A LEU* 3.8 4.7 - - - +
110A LYS* 1.3 78.8 - - - +
112A MET* 1.3 59.4 + - + +
113A GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 4.3 12.6 - - + -
49A THR* 3.8 35.9 - - + +
61A ILE* 4.3 4.9 - - + -
64A LEU* 4.0 30.3 - - + -
108A LEU* 2.7 44.0 + - + +
111A GLU* 1.3 76.1 - - + +
113A GLY* 1.3 63.2 + - - +
114A ILE* 3.5 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA 3.0 8.7 + - - -
110A LYS* 3.3 8.5 + - - -
111A GLU 3.3 4.2 + - - -
112A MET* 1.3 81.4 - - - +
114A ILE* 1.3 61.5 + - - +
----------------------------------------------------------
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