Contacts of the helix formed by residues 111 - 124 (chain B) in PDB entry 3D8U
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 111 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B SER* 3.1 13.4 + - - -
109B ASP* 2.7 17.0 + - - -
110B TYR* 1.3 72.0 - - - +
112B ILE* 1.3 62.7 + - - +
113B GLU* 3.2 9.2 + - - +
114B GLN* 2.9 35.0 + - - +
115B GLU* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR 4.1 2.3 + - - +
111B SER* 1.3 72.9 - - - +
113B GLU* 1.3 68.1 + - + +
115B GLU* 3.3 18.9 - - - +
116B GLU* 3.4 2.8 + - - +
136B GLU* 3.8 34.3 - - + +
137B HIS* 4.3 13.5 - - - +
138B SER* 3.0 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 3.1 6.6 + - - +
112B ILE* 1.3 85.0 - - + +
114B GLN* 1.3 64.2 + - - +
116B GLU* 3.1 25.6 - - - +
117B LYS* 3.3 6.8 + - - +
138B SER* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR 5.3 2.7 - - - +
108B SER* 4.4 12.1 - - - -
109B ASP 5.6 0.4 - - - +
111B SER* 2.9 27.0 + - - +
113B GLU* 1.3 69.5 - - - +
115B GLU* 1.3 57.6 + - - +
116B GLU 3.2 0.3 + - - -
117B LYS* 3.2 9.4 + - + +
118B LEU* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.9 26.5 - - + +
108B SER* 4.2 10.1 + - - +
111B SER 3.1 19.3 + - - +
112B ILE* 3.3 10.3 - - - +
114B GLN* 1.3 76.0 - - - +
116B GLU* 1.3 51.5 + - - +
118B LEU* 3.9 4.7 - - - +
119B LEU* 2.6 39.4 + - + +
132B LEU* 4.0 15.4 - - + +
133B PHE 4.4 4.2 + - - +
137B HIS* 3.0 41.6 + - - +
138B SER* 3.7 15.8 + - - -
141B THR* 3.9 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE 3.4 2.1 + - - -
113B GLU* 3.1 15.5 + - - +
115B GLU* 1.3 73.8 - - - +
117B LYS* 1.3 69.0 + - - +
118B LEU 2.9 1.4 + - - -
119B LEU* 3.0 1.1 + - - -
120B SER* 2.9 28.4 + - - -
138B SER* 2.9 37.0 - - - +
139B GLN* 4.4 1.0 + - - +
140B ARG* 3.2 33.8 + - + +
141B THR* 3.6 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN* 6.3 1.6 - - - +
113B GLU 3.3 7.0 + - - +
114B GLN* 3.2 13.5 + - - +
116B GLU* 1.3 78.9 - - - +
118B LEU* 1.3 58.4 + - - +
120B SER* 3.6 10.8 - - - -
121B THR* 3.1 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 4.8 8.3 - - + -
106B GLY* 5.8 3.1 - - - -
107B TYR 5.6 5.2 - - - +
108B SER* 6.5 0.2 - - - -
114B GLN 2.8 21.7 + - - +
115B GLU* 3.9 4.9 - - - +
117B LYS* 1.3 69.4 - - - +
119B LEU* 1.3 67.5 + - - +
120B SER 3.0 3.0 + - - -
121B THR* 3.0 19.7 + - - -
122B PHE* 3.2 28.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.8 14.7 - - + +
115B GLU* 2.6 25.6 + - + +
116B GLU 3.0 2.4 + - - +
118B LEU* 1.3 71.2 - - - +
120B SER* 1.3 63.4 - - - +
122B PHE* 2.9 16.3 + - - +
123B LEU* 2.9 24.4 + - - +
130B VAL* 6.1 3.1 - - + -
132B LEU* 6.0 2.7 - - + -
141B THR* 4.4 15.3 - - + -
144B LEU* 6.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU 2.9 16.5 + - - -
117B LYS* 3.6 8.1 - - - -
119B LEU* 1.3 76.9 - - - +
121B THR* 1.3 65.8 + - - +
123B LEU* 3.2 6.1 + - - +
124B GLU* 2.9 24.0 + - - +
144B LEU* 5.8 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A SER* 6.0 2.9 - - - +
102A GLN* 5.6 10.1 - - + +
117B LYS 3.1 16.3 + - - -
118B LEU* 3.0 8.8 + - - -
120B SER* 1.3 75.5 - - - +
122B PHE* 1.3 67.7 + - - +
124B GLU* 3.1 17.4 + - + +
125B SER* 3.3 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU 5.4 5.6 - - - -
104A LEU* 5.3 11.4 - - + -
74B ALA* 4.2 19.1 - - + -
76B ILE* 4.3 17.7 - - + -
104B LEU* 4.0 28.0 - - + -
105B LEU* 2.8 33.9 - - - -
106B GLY* 4.2 3.8 - - - -
118B LEU* 3.2 41.0 + - + -
119B LEU* 2.9 10.5 + - - +
121B THR* 1.3 78.8 - - - +
123B LEU* 1.3 64.2 + - - +
125B SER* 2.9 24.4 + - - -
126B ARG 3.5 8.9 + - - +
130B VAL* 6.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 2.9 11.7 + - + +
120B SER* 3.6 9.2 - - - +
122B PHE* 1.3 76.3 - - - +
124B GLU* 1.3 57.8 + - - +
125B SER 2.9 6.4 + - - -
126B ARG* 3.9 12.7 + - - +
127B PRO* 5.5 0.7 - - - +
144B LEU* 5.3 12.6 - - + +
148B SER* 5.3 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER 2.9 12.4 + - - +
121B THR* 3.1 13.6 + - + +
123B LEU* 1.3 74.8 - - - +
125B SER* 1.3 58.5 + - - +
----------------------------------------------------------
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