Contacts of the helix formed by residues 100 - 115 (chain A) in PDB entry 4OWW
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 GLU 100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A MET* 5.1 3.4 - - - +
96A LEU* 2.7 38.7 + - + +
97A ILE 4.3 1.6 - - - -
98A LEU 3.6 0.6 - - - -
99A THR* 1.3 93.3 + - - +
101A PRO* 1.3 69.5 - - - +
102A ALA* 3.3 4.7 + - + +
103A GLN* 3.1 31.1 + - + +
104A ALA* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR 3.8 7.0 - - - +
100A GLU* 1.3 87.2 - - - +
102A ALA* 1.3 62.9 + - - +
104A ALA* 3.1 14.2 + - - +
105A GLN* 4.5 5.4 + - - +
140A THR* 4.1 15.5 - - - +
144A GLN* 3.7 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 3.3 3.5 - - - +
101A PRO* 1.3 80.4 - - - +
103A GLN* 1.3 63.4 + - + +
105A GLN* 5.1 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 5.3 6.0 - - - +
96A LEU* 4.0 16.9 - - + +
100A GLU* 3.1 39.4 + - + +
102A ALA* 1.3 82.2 - - + +
104A ALA* 1.3 64.4 + - - +
105A GLN 3.4 2.5 - - - -
106A LYS* 3.3 16.3 + - + +
107A CYS* 3.0 36.9 + - - -
----------------------------------------------------------
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 ILE* 3.8 24.7 - - + +
100A GLU 3.1 9.3 + - - +
101A PRO 3.1 16.2 + - - +
102A ALA 3.4 0.2 - - - -
103A GLN* 1.3 76.3 - - - +
105A GLN* 1.3 64.7 + - + +
107A CYS* 3.4 2.3 + - - +
108A TYR* 3.0 25.8 + - - +
144A GLN* 3.5 25.8 - - - +
147A TRP* 3.9 10.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PRO 5.1 4.9 - - - +
102A ALA 5.7 2.9 - - - +
103A GLN 3.4 0.6 - - - -
104A ALA* 1.3 77.0 - - + +
106A LYS* 1.3 62.1 + - - +
108A TYR* 3.4 3.8 + - - +
109A ARG* 3.1 41.1 + - - +
147A TRP* 4.1 26.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
63A THR* 5.4 11.5 - - - +
68A GLU* 4.8 25.4 - - - +
71A ALA* 5.7 4.8 - - - +
72A ASN* 5.0 4.2 + - - +
75A LEU* 6.2 0.2 - - - +
93A LEU* 6.3 0.8 - - - +
103A GLN* 3.3 15.7 + - + +
104A ALA 3.3 0.4 - - - -
105A GLN* 1.3 75.5 - - - +
107A CYS* 1.3 71.7 + - - +
109A ARG* 3.0 33.3 + - - +
110A ASP* 2.8 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.9 22.7 - - + +
96A LEU* 3.6 38.1 - - - -
97A ILE* 3.7 21.5 - - + +
103A GLN* 3.0 33.1 + - - +
104A ALA 4.4 0.2 - - - -
106A LYS* 1.3 86.1 - - - +
108A TYR* 1.3 56.5 + - - +
110A ASP* 3.8 4.0 - - - +
111A LEU* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 4.0 10.7 - - + +
104A ALA 3.0 17.2 + - - +
105A GLN 3.6 5.2 - - - +
106A LYS 3.1 0.4 - - - -
107A CYS* 1.3 74.8 - - - +
109A ARG* 1.3 70.6 + - + +
111A LEU* 3.3 5.3 + - + -
112A ALA* 2.9 26.9 + - + +
119A MET* 3.8 23.8 - - + +
147A TRP* 4.0 13.9 - + + -
148A LEU* 3.8 31.2 - - + -
151A GLU* 3.5 34.7 + - + -
152A LEU* 3.9 14.1 - - + +
155A SER* 2.9 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLU* 5.8 2.2 + - - -
105A GLN* 3.1 32.2 + - - +
106A LYS* 3.0 34.1 + - - +
108A TYR* 1.3 81.5 - - + +
110A ASP* 1.3 66.7 + - - +
112A ALA* 3.3 6.4 + - - +
113A LEU* 3.1 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 3.2 27.3 + - - +
75A LEU* 4.0 16.2 - - + +
93A LEU* 4.1 15.0 - - + +
106A LYS* 2.8 43.2 + - - +
107A CYS* 3.8 6.0 - - - +
109A ARG* 1.3 79.3 + - - +
111A LEU* 1.3 57.9 + - - +
113A LEU* 3.0 12.7 + - - +
114A VAL* 2.8 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A CYS* 3.8 47.3 - - + +
93A LEU* 3.7 13.0 - - + +
94A PHE 4.6 2.5 - - - +
97A ILE* 4.1 20.9 - - + -
107A CYS 2.9 18.4 + - - +
108A TYR* 3.7 9.2 - - + +
110A ASP* 1.3 75.7 - - - +
112A ALA* 1.3 62.1 + - - +
114A VAL* 4.0 0.9 - - + -
115A SER* 3.1 34.5 + - - -
119A MET* 4.0 18.4 - - + -
122A VAL* 3.9 28.7 - - + -
148A LEU* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 2.9 23.1 + - + +
109A ARG* 3.6 7.2 - - - +
111A LEU* 1.3 76.0 - - - +
113A LEU* 1.3 65.5 + - + +
115A SER* 4.4 8.7 + - - +
119A MET* 3.6 26.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
76A ASN* 5.2 4.9 - - - +
109A ARG* 3.1 20.4 + - + +
110A ASP* 3.0 14.1 + - - +
112A ALA* 1.3 84.0 - - + +
114A VAL* 1.3 65.7 + - + +
115A SER 3.5 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.5 15.3 - - + -
76A ASN* 3.8 33.7 - - - +
79A VAL* 3.9 21.5 - - + +
86A HIS* 3.8 6.7 - - - -
89A ILE* 4.2 9.4 - - + -
90A CYS* 4.7 7.6 - - - -
93A LEU* 3.8 22.9 - - + -
110A ASP* 2.8 26.2 + - + +
111A LEU* 3.9 3.8 - - - +
113A LEU* 1.3 72.9 - - + +
115A SER* 1.3 67.8 + - - +
116A ARG* 3.2 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS* 3.8 6.0 + - - -
90A CYS* 4.2 10.7 - - - -
111A LEU* 3.1 21.6 + - - -
112A ALA 4.5 7.6 - - - +
113A LEU 3.3 7.1 - - - +
114A VAL* 1.3 77.3 - - - +
116A ARG* 1.3 56.9 + - - +
117A ASP* 2.9 16.6 + - - -
118A GLY* 4.6 3.4 + - - -
119A MET* 2.9 41.1 + - - -
----------------------------------------------------------
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