Contacts of the strand formed by residues 3 - 8 (chain B) in PDB entry 4F4W
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 VAL 3 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.8 21.3 - - + -
2B ILE* 1.3 76.4 - - - +
4B ILE* 1.3 75.6 + - - +
108B TYR* 4.2 18.8 - - + -
109B LEU 3.4 11.9 - - - +
110B ASP* 5.4 0.4 - - - -
144B GLY 3.6 0.7 - - - +
145B VAL* 3.3 8.6 - - - +
146B ALA 2.8 36.5 + - - +
148B ASN* 3.6 31.4 - - - +
149B LYS* 3.8 5.8 - - + +
152B ALA* 3.9 14.8 - - + -
238B ILE* 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ILE 4.2 0.2 + - - -
3B VAL* 1.3 78.4 - - - +
5B PHE* 1.3 61.2 + - - +
6B VAL* 4.2 11.9 - - + -
108B TYR* 3.6 0.3 - - - -
109B LEU* 2.8 48.7 + - + +
111B VAL* 3.8 33.0 - - + -
122B GLY 3.8 23.1 - - - +
125B LEU* 4.0 15.3 - - + -
126B ALA* 4.1 6.3 - - + +
129B ILE* 4.0 14.6 - - + -
143B VAL* 3.6 26.9 - - + -
144B GLY 3.4 3.1 - - - +
145B VAL* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL 4.1 0.8 - - - -
4B ILE* 1.3 74.8 - - - +
6B VAL* 1.3 60.5 + - - +
7B ASP* 3.6 24.9 - - + -
106B GLU* 3.4 46.7 - - + -
107B ALA 3.4 13.5 - - - -
108B TYR* 3.3 38.4 - + + +
143B VAL* 3.2 8.7 - - - +
144B GLY 2.8 31.2 + - - +
152B ALA* 3.6 22.6 - - + +
153B LYS* 3.6 27.1 - - + -
156B ALA* 3.5 25.8 - - + -
157B ASP* 5.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.2 13.0 - - + -
5B PHE* 1.3 81.9 - - - +
7B ASP* 1.3 63.3 + - - +
8B PHE* 4.0 17.4 - - + -
92B LEU* 4.0 30.5 - - + -
105B ASP 4.4 0.2 - - - -
106B GLU* 3.0 8.7 - - - +
107B ALA 2.9 33.2 + - - +
109B LEU* 4.2 10.3 - - + -
129B ILE* 4.7 2.9 - - + -
133B ILE* 4.6 5.2 - - + -
141B VAL* 3.9 30.3 - - + -
142B THR 3.6 2.7 - - - -
143B VAL* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.6 22.6 - - + -
6B VAL* 1.3 76.6 - - - +
8B PHE* 1.3 64.7 + - - +
9B ASP* 3.5 2.1 + - - +
105B ASP* 3.4 3.1 - - - +
106B GLU* 3.5 8.8 - - - +
141B VAL* 4.4 0.2 - - - -
142B THR* 2.9 35.4 + - - +
153B LYS* 4.6 2.6 + - - -
156B ALA* 5.3 1.3 - - + -
157B ASP* 4.5 2.6 - - - +
160B LYS* 3.4 26.0 + - - -
401B DCP 3.5 1.4 + - - -
402B CA 2.2 31.9 - - - -
403B CA 2.9 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.0 18.4 - - + -
7B ASP* 1.3 73.7 + - - +
9B ASP* 1.3 62.2 + - - +
11B PHE* 3.6 37.2 + + + -
85B SER* 4.2 4.7 - - - -
88B ILE* 3.3 44.6 - - + -
89B MET* 3.5 23.8 - - + -
92B LEU* 4.6 2.5 - - + -
104B ILE 3.6 17.9 - - - -
105B ASP* 2.9 37.0 + - + +
106B GLU 5.9 0.2 - - - -
139B ILE* 4.6 3.6 - - + -
141B VAL* 3.6 23.1 - - + -
401B DCP 3.3 0.9 + - - -
402B CA 2.4 30.0 - - - -
----------------------------------------------------------
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