Contacts of the helix formed by residues 101 - 115 (chain A) in PDB entry 1W3U
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 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A MET* 3.7 0.6 - - - +
100A THR* 1.3 80.5 - - - +
102A SER* 1.3 65.6 + - - -
103A TRP 3.3 2.6 + - - -
104A ALA 3.4 0.7 + - - -
105A SER* 2.9 27.9 + - - -
128A TYR* 3.4 24.8 - - - -
152A GLU* 3.3 3.7 + - - -
155A GLU* 3.3 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLY* 1.3 71.9 - - - -
103A TRP* 1.3 63.9 + - - +
105A SER* 3.4 6.5 + - - -
106A LYS* 3.1 27.6 + - - +
152A GLU* 4.8 0.2 - - - -
154A ILE* 3.5 34.0 - - - +
155A GLU* 2.5 35.0 + - - -
330A SER* 4.1 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 4.5 5.4 - - - -
81A PHE* 3.6 25.2 - + - -
102A SER* 1.3 74.8 - - - +
104A ALA* 1.3 67.9 + - - +
106A LYS* 3.3 24.1 + - + +
107A ALA* 3.0 22.2 + - - +
149A THR* 4.1 7.4 - - + -
152A GLU* 2.9 11.1 + - - +
153A THR* 3.6 27.6 - - - +
154A ILE* 3.7 28.5 - - + +
173A ASP* 4.4 1.3 - - - +
328A HIS* 5.9 2.2 - + - -
1363A PLP 3.4 85.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 4.7 2.6 - - + -
98A VAL 3.4 25.1 - - - +
99A MET* 3.7 9.5 - - + +
100A THR* 3.5 13.2 - - - +
101A GLY 3.8 2.0 - - - +
103A TRP* 1.3 76.4 - - - +
105A SER* 1.3 57.1 + - - +
107A ALA* 3.0 6.3 + - - +
108A LEU* 2.9 29.8 + - - +
147A HIS* 5.5 2.0 - - - +
149A THR* 3.6 13.6 + - - +
152A GLU* 3.0 22.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
99A MET* 3.6 17.9 - - - +
101A GLY 2.9 19.8 + - - -
102A SER* 3.7 7.6 - - - -
103A TRP 3.2 0.4 - - - -
104A ALA* 1.3 76.2 - - - +
106A LYS* 1.3 64.0 + - - +
108A LEU* 3.4 2.5 + - - +
109A LYS* 3.0 26.0 + - - +
128A TYR* 4.4 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.6 23.1 - - + -
102A SER* 3.1 18.8 + - - +
103A TRP* 3.7 23.8 - - + +
104A ALA 3.2 0.4 - - - -
105A SER* 1.3 77.6 - - - +
107A ALA* 1.3 64.0 + - - +
109A LYS* 3.4 32.5 + - - +
110A GLU* 3.3 25.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
81A PHE* 3.6 32.2 - - + +
97A TYR* 3.8 12.3 + - + +
103A TRP 3.0 12.0 + - - +
104A ALA 3.0 9.2 + - - +
106A LYS* 1.3 77.8 - - - +
108A LEU* 1.3 63.4 + - - +
110A GLU* 3.3 5.0 + - - +
111A ALA* 3.2 20.6 + - - +
147A HIS* 3.7 26.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
97A TYR* 3.8 26.6 - - + -
99A MET* 3.7 29.4 - - + -
104A ALA 2.9 15.5 + - - +
105A SER 3.7 4.3 - - - +
107A ALA* 1.3 78.3 - - - +
109A LYS* 1.3 64.4 + - - +
111A ALA* 3.0 2.4 + - - +
112A LYS* 3.0 42.7 + - - +
117A THR* 3.6 33.2 - - + +
118A HIS 5.1 1.3 - - - +
119A VAL* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER 3.0 16.9 + - - +
106A LYS* 3.6 36.5 - - - +
108A LEU* 1.3 78.4 - - - +
110A GLU* 1.3 78.5 + - - +
112A LYS* 3.4 21.6 + - + +
113A LEU* 3.7 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER 4.7 3.6 - - - +
81A PHE* 3.5 46.4 - - + +
82A ALA* 4.2 14.4 - - + +
106A LYS 3.3 7.8 + - - +
107A ALA 3.8 2.0 - - - +
108A LEU 3.2 0.6 - - - -
109A LYS* 1.3 93.3 + - - +
111A ALA* 1.3 67.4 + - - +
113A LEU* 3.0 44.6 + - - +
114A ILE* 3.7 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE 4.3 0.6 + - - -
85A PRO* 3.9 19.3 - - + -
89A LEU* 4.1 1.2 - - - +
95A ALA* 4.5 2.0 - - + -
97A TYR* 3.2 41.5 - - + +
107A ALA 3.2 2.8 + - - +
108A LEU 3.0 9.2 + - - +
110A GLU* 1.3 78.7 - - - +
112A LYS* 1.3 57.9 + - - +
114A ILE* 2.8 19.8 + - - +
115A GLY 3.1 12.5 + - - +
117A THR* 3.7 10.9 - - + +
145A TYR* 4.2 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 3.0 39.8 + - + +
109A LYS* 3.6 14.4 - - + +
110A GLU 3.1 0.2 - - - -
111A ALA* 1.3 76.5 - - - +
113A LEU* 1.3 61.7 + - + +
114A ILE 3.3 0.3 + - - -
115A GLY* 3.6 16.6 + - - +
117A THR* 3.3 28.3 - - + +
119A VAL* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LYS 3.7 7.4 + - - +
110A GLU* 3.0 42.1 + - - +
112A LYS* 1.3 79.3 - - + +
114A ILE* 1.3 71.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 4.3 7.6 - - + +
85A PRO* 3.7 46.4 - - + +
86A MET* 3.8 32.3 - - + +
89A LEU* 4.4 10.6 - - + +
110A GLU 3.7 13.2 - - - +
111A ALA 2.8 6.3 + - - +
113A LEU* 1.3 93.4 - - + +
115A GLY* 1.3 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.4 13.8 - - - +
111A ALA 3.1 13.5 + - - +
112A LYS* 3.6 10.9 + - - +
113A LEU 3.6 1.4 - - - -
114A ILE* 1.3 80.9 - - - +
116A ASP* 1.3 67.2 + - - -
117A THR* 3.6 5.0 + - - +
----------------------------------------------------------
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