Contacts of the helix formed by residues 103 - 119 (chain B) in PDB entry 4D8D
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 SER 103 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE 3.6 4.9 + - - -
102B HIS* 1.3 80.7 + - - +
104B GLN* 1.3 57.6 + - - +
105B ARG* 3.4 11.3 + - - +
106B ARG* 2.9 36.7 + - - +
107B GLN* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B HIS* 3.9 13.1 - - + -
103B SER* 1.3 73.7 - - - +
105B ARG* 1.3 56.5 + - - +
107B GLN* 3.7 27.4 + - - +
108B ASP* 2.7 55.9 + - - +
123D ASP* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B SER* 3.6 9.0 - - - +
104B GLN* 1.3 80.6 - - - +
106B ARG* 1.3 56.3 + - + +
108B ASP* 3.3 5.3 + - - +
109B ILE* 2.9 41.3 + - + +
76D LEU* 4.3 14.5 - - - +
121D PHE* 3.5 46.6 - - - +
123D ASP* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.6 21.4 - - + +
101B ILE* 2.8 65.5 + - - +
103B SER* 2.9 30.2 + - - +
105B ARG* 1.3 73.9 - - + +
107B GLN* 1.3 64.6 + - - +
109B ILE* 3.4 11.9 + - + +
110B LEU* 3.0 23.6 + - - +
183B TRP* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B HIS* 2.7 34.2 + - + +
103B SER 2.9 12.2 + - - +
104B GLN* 3.5 28.8 + - - +
106B ARG* 1.3 76.3 - - - +
108B ASP* 1.3 58.5 + - - +
110B LEU* 3.2 4.8 + - - +
111B ASP* 2.9 38.8 + - - +
125B GLN* 2.9 46.5 + - - +
126B ASN* 4.6 6.9 + - - +
127B TYR* 3.6 14.5 - - - -
183B TRP* 3.8 10.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLN* 2.7 50.7 + - - +
105B ARG* 3.6 2.4 - - - +
107B GLN* 1.3 77.6 + - - +
109B ILE* 1.3 56.8 + - - +
111B ASP* 3.2 9.3 + - - +
112B LEU* 2.9 35.1 + - + +
121D PHE* 3.6 32.0 - - + -
122D PRO* 4.8 6.0 - - + +
123D ASP* 4.0 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 2.9 39.2 + - + +
106B ARG* 3.7 11.4 - - + +
108B ASP* 1.3 76.7 - - - +
110B LEU* 1.3 64.5 + - - +
112B LEU* 3.3 6.4 + - - +
113B TRP* 2.9 25.6 + - + +
121D PHE* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 4.7 10.5 - - + -
97B LEU* 4.3 30.7 - - + -
106B ARG 3.0 13.6 + - - +
107B GLN* 3.2 6.3 + - - +
109B ILE* 1.3 77.7 - - - +
111B ASP* 1.3 63.4 + - - +
113B TRP* 3.2 25.3 + - + +
114B ILE* 2.9 47.9 + - + +
125B GLN* 3.4 31.6 - - - +
141B TRP* 4.6 4.3 - - + -
183B TRP* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLN* 2.9 19.8 + - - +
108B ASP* 3.5 13.5 - - - +
110B LEU* 1.3 76.6 - - - +
112B LEU* 1.3 57.2 + - + +
114B ILE* 3.3 6.9 + - - +
115B TYR* 2.8 30.1 + - - +
120B TYR 4.9 0.3 - - - +
122B PRO* 3.9 31.0 - - + +
123B ASP* 5.6 0.2 - - - -
124B TRP* 4.3 10.6 + - - +
125B GLN* 2.5 48.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASP* 2.9 21.2 + - + +
109B ILE* 3.7 5.4 - - - +
111B ASP* 1.3 70.5 - - + +
113B TRP* 1.3 61.3 + - - +
115B TYR* 3.5 13.2 - - + +
116B HIS* 2.8 31.9 + - - +
122B PRO* 4.9 6.1 - - + -
76D LEU* 5.8 0.4 - - + -
112D LEU* 3.9 28.0 - - + -
115D TYR* 4.1 31.9 - - + +
121D PHE* 3.8 30.3 - - + -
122D PRO* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.4 37.2 - + - -
69B PRO* 4.8 19.5 - - + +
91B LEU* 4.5 13.9 - - + -
94B LYS* 3.4 31.6 - - + -
109B ILE* 2.9 20.1 + - + +
110B LEU* 3.2 22.4 + - + +
112B LEU* 1.3 76.0 - - - +
114B ILE* 1.3 54.7 + - + +
116B HIS* 3.7 3.4 - - + +
117B THR* 2.7 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 4.0 21.1 - - + -
87B LEU* 4.3 13.0 - - + -
91B LEU* 4.5 11.0 - - + -
110B LEU* 2.9 45.5 + - + +
111B ASP 3.8 3.4 - - - +
113B TRP* 1.3 76.1 - - + +
115B TYR* 1.3 58.1 + - - +
117B THR* 3.6 5.6 - - - -
118B GLN* 2.8 33.3 + - + +
119B GLY 3.3 1.6 + - - -
120B TYR* 3.9 28.7 + - + -
124B TRP* 3.8 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 3.2 33.9 + - - +
74B VAL 5.9 0.4 - - - -
76B LEU* 3.7 26.9 - - + +
111B ASP 2.8 18.6 + - - +
112B LEU* 3.5 20.4 - - + +
114B ILE* 1.3 78.2 - - - +
116B HIS* 1.3 61.2 + - + +
119B GLY* 2.9 30.2 + - - +
120B TYR 3.3 28.7 - - - +
121B PHE* 5.3 0.9 - - - -
122B PRO* 3.6 20.0 - - + -
112D LEU* 4.1 21.9 - - + +
115D TYR* 6.2 0.4 - + - -
116D HIS* 3.5 25.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 3.9 29.7 + - + -
71B THR* 2.5 40.2 + - - -
72B PRO* 4.6 1.1 - - + +
73B GLN* 3.2 51.9 + - + +
74B VAL* 3.6 13.5 + - - +
112B LEU 2.8 20.6 + - - +
113B TRP* 3.7 5.6 - - + +
115B TYR* 1.3 78.6 - - + +
117B THR* 1.3 69.0 + - + +
73D GLN* 5.4 15.8 - - + +
116D HIS* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 4.3 7.4 + - - -
96A TRP* 3.5 24.4 - - + +
69B PRO* 5.9 1.1 - - + -
71B THR* 4.7 9.6 - - - +
74B VAL* 3.6 17.8 - - - +
113B TRP* 2.7 48.2 + - + +
114B ILE 3.6 0.2 + - - -
116B HIS* 1.3 89.6 - - + +
118B GLN* 1.3 82.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 4.0 13.1 + - - -
94A GLU 4.6 3.4 + - - -
96A TRP* 3.3 63.1 + - + +
97A THR* 5.0 5.5 - - - +
100A ASP* 4.0 3.1 - - - +
119A TRP* 3.7 1.8 - - - -
74B VAL* 3.5 7.4 - - - -
77B ARG* 2.8 48.7 + - - +
87B LEU* 5.2 1.6 - - + -
114B ILE* 2.8 18.8 + - + +
117B THR* 1.3 97.1 + - - +
119B GLY* 1.3 58.1 + - - +
120B TYR* 3.2 26.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 5.0 0.2 - - - -
74B VAL* 3.3 8.8 - - - +
75B PRO 3.4 18.8 - - - -
76B LEU* 3.3 10.1 - - - +
77B ARG 3.0 23.8 + - - -
114B ILE 3.3 0.4 + - - -
115B TYR* 2.9 21.9 + - - -
118B GLN* 1.3 76.7 - - - +
120B TYR* 1.3 64.0 + - - +
121B PHE 3.2 2.6 + - - -
----------------------------------------------------------
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