Contacts of the strand formed by residues 4 - 10 (chain F) in PDB entry 3CB4
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 4 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 3.1 31.6 + - - +
3F ASN* 1.3 81.9 - - + +
5F ARG* 1.3 80.3 + - - +
6F ASN* 3.3 21.5 - - - +
72F GLN* 3.2 26.9 - - + +
74F ASN* 3.5 14.4 - - - +
182F PRO* 3.6 0.2 - - - +
183F PRO* 3.2 23.1 - - + +
251F LYS* 5.6 2.5 - - + -
252F CYS 3.9 10.8 - - - +
253F GLY* 3.3 17.5 - - - +
254F GLU* 3.9 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 5 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LYS 3.0 26.1 + - - -
3F ASN* 4.0 6.5 - - - +
4F ILE* 1.3 90.9 + - - +
6F ASN* 1.3 64.3 + - - +
7F PHE* 3.6 6.6 - - - -
71F TYR* 3.9 8.4 + - + -
72F GLN 2.9 9.3 + - - -
73F LEU* 3.6 25.9 - - + -
74F ASN 3.1 24.1 + - - +
176F LEU* 3.8 10.8 - - + -
177F VAL* 2.9 55.3 + - + +
180F ILE* 2.9 32.1 + - + -
181F PRO 4.6 1.8 - - - -
182F PRO* 3.7 15.4 - - - +
183F PRO* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 6 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ILE* 3.3 19.7 - - - +
5F ARG* 1.3 71.2 - - - +
7F PHE* 1.3 64.7 + - - +
74F ASN* 3.2 21.0 - - + +
76F ILE* 5.6 1.1 - - + -
94F ALA 3.7 15.0 - - - +
95F CYS* 4.0 3.4 - - - -
96F GLU* 3.2 31.0 + - - +
97F GLY 3.5 4.3 + - - -
180F ILE* 4.0 7.5 - - - +
181F PRO 5.5 0.2 + - - -
183F PRO* 4.0 4.6 - - - +
211F ARG* 3.2 35.2 - - - +
253F GLY 3.2 19.5 + - - +
255F VAL* 4.1 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 7 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ARG 3.6 17.0 - - - -
6F ASN* 1.3 75.4 - - - +
8F SER* 1.3 66.4 + - - +
9F ILE* 4.2 6.7 - - + -
24F ILE* 4.8 8.5 - - + -
73F LEU* 4.2 19.3 - - + -
74F ASN 3.2 3.8 + - - +
75F PHE* 3.1 42.4 - + + +
76F ILE 3.0 21.3 + - - -
95F CYS* 3.6 9.1 - - - -
97F GLY 3.2 15.9 - - - +
98F ALA* 4.3 1.1 - - - -
99F LEU* 3.6 37.9 - - + -
176F LEU* 3.4 35.0 - - + -
180F ILE* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 8 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F PHE* 1.3 77.1 - - - +
9F ILE* 1.3 65.1 + - - +
10F ILE* 4.0 0.8 - - - +
75F PHE* 5.0 0.2 - - - -
76F ILE* 3.1 22.2 - - - -
78F THR* 3.2 15.3 - - - -
91F SER* 5.5 1.3 - - - -
92F LEU* 3.3 29.0 - - - +
95F CYS* 3.6 13.8 - - - -
97F GLY 3.5 3.7 + - - -
98F ALA* 3.3 8.5 - - - +
99F LEU 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F PHE* 4.2 5.6 - - + -
8F SER* 1.3 77.1 - - - +
10F ILE* 1.3 62.5 + - - +
11F ALA* 3.8 14.6 + - + +
20F LEU* 5.0 4.3 - - + -
21F SER* 4.1 17.9 - - - +
24F ILE* 4.0 27.1 - - + -
75F PHE* 3.9 28.0 - - + -
76F ILE 3.6 7.4 + - - +
77F ASP* 4.5 6.0 - - - +
78F THR* 3.7 23.4 + - - +
99F LEU* 3.7 21.3 - - + -
101F VAL* 3.7 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F SER 5.0 0.2 - - - +
9F ILE* 1.3 71.5 - - - +
11F ALA* 1.3 61.7 + - - +
78F THR* 4.7 14.4 - - + +
92F LEU* 4.9 5.4 - - + -
98F ALA* 4.5 15.0 - - + -
99F LEU 2.9 12.7 + - - +
100F LEU* 3.6 11.9 - - + +
101F VAL 3.1 25.9 + - - +
112F THR* 3.5 37.1 - - + +
115F ASN* 3.7 37.2 - - + +
116F CYS* 3.8 17.3 - - + -
119F ALA* 4.2 11.7 - - + -
126F VAL* 5.4 2.5 - - + -
----------------------------------------------------------
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