Contacts of the strand formed by residues 116 - 123 (chain B) in PDB entry 6DC0
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 116 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 2.6 39.7 + - + -
108B ALA 3.5 11.2 - - - +
109B LEU* 3.8 20.6 - - + +
114B GLY 3.5 3.8 + - - +
115B ARG* 1.3 73.6 - - - +
117B LEU* 1.3 60.8 + - - +
118B ARG* 3.2 19.3 + - - +
161B GLU* 5.0 2.1 - - - +
162B LYS* 2.6 59.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 3.9 29.2 - - + +
108B ALA* 2.8 36.0 + - + +
115B ARG* 3.7 44.9 - - + +
116B GLU* 1.3 71.2 - - - +
118B ARG* 1.3 86.6 + - - +
147B VAL* 3.8 22.0 - - + -
159B PHE* 4.5 7.6 - - + -
160B PHE 3.5 15.3 - - - +
161B GLU* 3.7 21.3 - - - +
162B LYS 4.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.4 32.3 - - - +
105B VAL* 4.1 13.7 - - + -
106B SER 3.8 2.5 - - - -
107B ARG* 3.8 19.8 - - - +
116B GLU* 3.2 36.0 + - - +
117B LEU* 1.3 110.9 + - - +
119B CYS* 1.3 58.8 + - - +
120B LYS* 4.3 0.9 - - + -
159B PHE* 3.5 3.5 - - - -
160B PHE* 2.6 53.5 + - + +
161B GLU 4.5 2.8 - - - +
162B LYS* 3.6 34.5 - - + +
163B ASP* 5.3 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.9 22.2 - - + -
104B HIS 3.7 1.4 - - - +
105B VAL* 3.4 3.6 - - - +
106B SER* 2.9 38.0 + - - +
108B ALA* 4.1 7.6 - - + -
118B ARG* 1.3 75.2 - - - +
120B LYS* 1.3 64.4 + - - +
121B VAL* 5.2 0.9 - - - +
157B TYR* 3.9 21.3 - - - -
158B VAL 3.4 7.0 - - - -
159B PHE* 3.3 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B HIS 3.8 6.1 - - - +
105B VAL* 4.1 23.3 - - + +
118B ARG* 4.3 0.6 - - + -
119B CYS* 1.3 73.7 - - - +
121B VAL* 1.3 60.5 + - - +
122B PHE* 3.9 22.3 + - + -
156B ALA 4.0 0.5 - - - +
157B TYR* 3.7 1.4 - - - -
158B VAL* 2.9 35.6 + - + +
160B PHE* 3.9 30.5 - - + -
224B GLU* 5.3 1.8 + - - +
225B SER* 3.3 21.6 + - - -
227B GLU* 3.3 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 6.0 2.2 - - + -
104B HIS* 3.2 49.6 + - + +
119B CYS* 3.9 2.0 + - - +
120B LYS* 1.3 72.8 - - - +
122B PHE* 1.3 63.6 - - - +
123B PRO* 4.7 0.7 - - - +
155B LYS* 3.6 31.8 + - + +
156B ALA 3.3 10.1 - - - +
157B TYR* 3.3 36.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
120B LYS* 3.9 28.3 - - + -
121B VAL* 1.3 77.7 - - - +
123B PRO* 1.3 74.7 - - + +
126B HIS* 4.9 1.1 - - + -
127B TYR* 4.0 24.5 - - + +
130B LYS* 3.6 35.9 - - + -
131B ILE* 5.0 3.1 - - + -
155B LYS* 3.1 10.7 - - - +
156B ALA 2.7 36.2 + - - +
158B VAL* 3.6 33.0 - - + -
160B PHE* 6.1 0.7 - + - -
227B GLU* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL 4.7 0.7 - - - +
122B PHE* 1.3 87.7 - - + +
124B ILE* 1.4 67.5 + - - +
125B LYS* 3.1 6.5 - - + +
126B HIS* 2.9 32.8 + - + +
127B TYR 3.3 8.1 + - - -
154B THR* 3.5 15.0 - - + +
155B LYS* 4.2 4.4 - - + +
----------------------------------------------------------
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