Contacts of the helix formed by residues 103 - 116 (chain D) in PDB entry 3SDL
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 103 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D THR 4.7 4.9 - - - +
102D GLN* 1.3 77.9 - - - +
104D VAL* 1.3 64.7 + - - +
105D ALA* 3.7 5.1 + - - +
106D HIS* 3.1 25.9 + - - +
107D LEU* 3.1 17.8 + - - +
133D ASP 3.5 12.6 - - - +
134D GLN* 4.6 9.0 - - - +
135D LEU 3.3 13.7 - - - +
136D PRO* 4.9 1.8 - - + -
137D LEU* 3.8 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D THR* 1.3 73.3 - - - +
105D ALA* 1.3 57.0 + - - +
107D LEU* 3.2 3.2 + - - +
108D LYS* 2.8 44.4 + - + +
124D LEU* 5.1 2.0 - - + -
131D LEU* 3.5 39.0 - - + +
132D GLU 2.9 35.7 - - - +
133D ASP* 3.4 4.2 + - - +
135D LEU 2.7 15.8 + - - +
137D LEU* 3.8 20.0 - - + -
140D TYR* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D THR* 3.2 5.4 - - - +
104D VAL* 1.3 78.7 - - - +
106D HIS* 1.3 61.7 + - - +
108D LYS* 3.3 8.7 + - - +
109D GLN* 3.0 27.6 + - - +
119D ASP* 5.9 0.3 - - - +
133D ASP* 2.8 40.0 + - + +
134D GLN* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLN* 3.7 43.0 + - + +
103D THR* 3.1 29.5 + - - +
105D ALA* 1.3 77.9 - - - +
107D LEU* 1.3 64.5 + - - +
109D GLN* 3.0 22.9 + - + +
110D GLN* 3.3 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ILE* 4.0 23.8 - - + -
86D VAL* 4.5 4.7 - - + -
96D TYR* 4.5 11.7 - - + -
98D VAL* 3.8 23.6 - - + -
103D THR 3.1 8.4 + - - +
104D VAL* 3.2 7.4 + - - +
106D HIS* 1.3 82.5 + - - +
108D LYS* 1.3 64.5 + - - +
110D GLN* 2.9 21.1 + - + +
111D VAL* 3.0 21.1 + - + +
124D LEU* 3.6 25.1 - - + -
131D LEU* 4.7 8.5 - - + -
137D LEU* 3.9 26.5 - - + -
142D LEU* 5.1 0.9 - - + -
148D VAL* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D VAL* 2.8 27.4 + - + +
105D ALA* 3.5 6.3 - - - +
107D LEU* 1.3 75.8 - - - +
109D GLN* 1.3 56.7 + - - +
111D VAL* 4.3 4.7 - - - -
112D SER* 2.8 30.7 + - - -
119D ASP* 3.1 27.3 + - + +
120D ASP* 5.2 1.2 - - - +
122D PHE* 3.0 49.2 + - + -
123D TRP* 4.4 5.1 - - - +
124D LEU* 3.8 27.4 - - + +
131D LEU 5.9 0.7 - - - +
133D ASP* 3.8 34.2 + - - +
153D ARG* 4.9 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ALA* 3.0 14.4 + - - +
106D HIS* 3.0 17.6 + - + +
108D LYS* 1.3 76.2 - - - +
110D GLN* 1.3 58.5 + - + +
112D SER* 3.4 10.1 + - - -
113D GLY* 3.0 24.3 + - - -
119D ASP* 4.4 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D TYR* 3.7 26.0 - - + +
97D GLU* 3.0 29.7 + - - +
98D VAL* 3.7 15.0 - - - +
102D GLN* 4.6 1.0 + - - +
106D HIS* 3.3 27.8 + - + +
107D LEU* 2.9 10.9 + - + +
109D GLN* 1.3 76.3 - - + +
111D VAL* 1.3 65.9 + - - +
113D GLY* 3.1 3.0 + - - -
114D LEU* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D VAL* 3.7 39.7 - - + -
96D TYR* 3.5 15.0 - - + +
107D LEU* 3.0 21.3 + - + +
108D LYS* 3.8 7.4 - - - +
110D GLN* 1.3 74.5 - - - +
112D SER* 1.3 58.0 + - - +
114D LEU* 3.3 0.3 + - - -
115D GLU* 2.8 37.4 + - + +
122D PHE* 3.9 14.6 - - + -
124D LEU* 4.5 5.4 - - + -
150D MET* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D LYS 2.8 20.1 + - - -
109D GLN* 3.5 16.3 + - - -
111D VAL* 1.3 77.3 - - - +
113D GLY* 1.3 56.6 + - - +
115D GLU* 5.1 0.4 - - - -
116D GLY* 2.8 27.5 + - - -
117D VAL 2.7 32.6 + - - +
118D GLN* 3.9 7.4 + - - -
119D ASP* 3.7 18.2 + - - +
122D PHE* 4.0 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D GLN 3.0 14.7 + - - -
110D GLN* 3.1 3.1 + - - -
112D SER* 1.3 76.9 + - - +
114D LEU* 1.3 61.6 + - - +
116D GLY* 3.8 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D ARG* 3.7 18.8 + - - +
94D SER* 3.2 26.9 - - - +
95D THR 5.0 3.6 - - - +
96D TYR* 3.4 29.4 - - + +
110D GLN 3.0 11.7 + - - +
113D GLY* 1.3 80.0 - - - +
115D GLU* 1.3 84.4 + - - +
116D GLY* 3.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D VAL* 5.0 2.5 - - + +
88D ASN* 3.1 42.2 + - - +
92D ARG* 3.7 12.9 + - - +
94D SER* 4.7 3.8 - - - -
96D TYR* 4.1 3.3 + - - +
111D VAL* 2.8 27.7 + - + +
114D LEU* 1.3 94.1 - - + +
116D GLY* 1.3 62.1 + - - +
117D VAL* 3.4 13.5 + - + +
150D MET* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D SER 2.8 11.9 + - - -
113D GLY 3.8 4.7 + - - -
114D LEU 3.3 4.0 + - - -
115D GLU* 1.3 78.4 - - - +
117D VAL* 1.3 60.4 + - - +
118D GLN* 4.2 3.5 + - - -
----------------------------------------------------------
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