Contacts of the strand formed by residues 106 - 115 (chain B) in PDB entry 5C16
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 ILE 106 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 4.9 10.3 - - + +
100B LEU* 3.8 36.1 - - + +
105B SER* 1.3 73.5 - - - +
107B LYS* 1.3 66.1 + - - +
108B ALA 3.8 21.1 - - - +
109B ILE* 3.8 24.5 - - + -
128B THR* 4.0 16.6 - - + -
129B VAL 4.1 2.7 - - - -
130B THR* 4.4 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 3.8 26.3 - - - +
106B ILE* 1.3 77.4 + - - +
108B ALA* 1.3 65.0 + - - +
129B VAL* 2.9 16.7 + - + +
130B THR 3.9 13.5 - - - -
131B ASP* 3.9 21.9 + - - +
194B LEU* 5.0 4.9 - - - +
199B ASN* 4.3 7.5 - - - +
203B HIS* 3.5 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 3.7 2.3 - - - +
107B LYS* 1.3 82.3 - - - +
109B ILE* 1.3 71.8 + - - +
110B VAL* 5.4 2.5 - - + -
127B LEU 4.4 0.9 - - - -
128B THR* 3.4 2.6 - - - +
129B VAL* 2.9 39.5 + - + +
194B LEU* 4.0 30.1 - - + -
196B ILE* 6.5 0.4 - - - -
199B ASN* 4.2 13.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
98B ALA* 6.4 0.4 - - + -
106B ILE* 3.8 29.2 - - + -
108B ALA* 1.3 82.5 - - - +
110B VAL* 1.3 70.0 + - - +
111B LYS* 4.6 9.7 - - + +
126B THR* 3.7 23.3 - - + -
127B LEU 3.3 4.7 - - - +
128B THR* 3.9 11.2 - - + +
194B LEU* 5.4 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA* 5.4 2.0 - - + -
109B ILE* 1.3 81.4 - - - +
111B LYS* 1.3 72.6 + - - +
112B ASP 5.1 0.7 - - - +
113B VAL* 3.7 23.2 - - + +
125B GLY 4.0 0.3 - - - +
126B THR* 4.1 0.9 - - - -
127B LEU* 2.4 51.6 + - + +
186B TYR* 6.2 4.7 - - + -
194B LEU* 4.5 17.0 - - + -
196B ILE* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 4.6 8.1 - - + +
110B VAL* 1.3 87.4 - - - +
112B ASP* 1.3 80.0 + - - +
113B VAL 3.3 1.1 + - - -
125B GLY 3.7 1.1 - - - -
126B THR* 3.2 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 5.1 0.3 - - - +
111B LYS* 1.3 80.7 - - - +
113B VAL* 1.3 61.3 + - - +
114B MET* 5.6 2.0 - - - +
124B SER* 5.1 11.6 - - - -
125B GLY 3.0 13.9 + - - +
186B TYR 4.7 10.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 3.7 20.9 - - + +
112B ASP* 1.3 77.7 - - - +
114B MET* 1.3 68.9 + - - +
115B TYR 4.5 0.2 - - - +
123B VAL 3.3 2.4 - - - +
124B SER* 3.6 1.6 - - - -
125B GLY 2.9 27.9 + - - +
127B LEU* 4.0 21.1 - - + -
136B PHE* 3.3 26.8 - - + -
184B LEU* 4.6 11.0 - - + -
185B ALA 3.9 9.4 - - - +
186B TYR* 5.3 3.8 - - + -
196B ILE* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP 4.4 1.8 + - - +
113B VAL* 1.3 75.7 - - - +
115B TYR* 1.3 59.6 + - - +
116B ILE* 3.6 3.0 - - + +
122B ALA* 3.8 27.1 - - + -
123B VAL* 3.5 24.7 - - - +
124B SER* 3.8 12.6 - - - +
184B LEU* 3.3 4.7 - - - -
185B ALA* 2.5 59.8 + - + +
186B TYR 5.2 4.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
113B VAL 3.7 2.0 + - - -
114B MET* 1.3 69.7 - - - +
116B ILE* 1.3 66.1 + - - +
117B CYS* 3.0 31.6 + - + -
118B PRO* 4.2 13.7 - - - +
121B GLY 3.9 0.3 - - - +
122B ALA* 3.8 0.7 - - - -
123B VAL* 3.2 28.7 + - + +
136B PHE* 3.8 22.8 - - + -
145B PHE* 3.7 35.4 - + - -
147B LEU* 3.8 29.8 - - + +
181B ASN 4.8 2.6 + - - -
182B LEU* 4.3 9.7 - - + +
183B ARG 3.5 22.2 - - - -
184B LEU* 3.8 18.8 - - + -
392B TYR* 4.4 8.8 + - - -
----------------------------------------------------------
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