Contacts of the strand formed by residues 4 - 10 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 2.9 28.9 + - - +
3E ASN* 1.3 81.4 - - - +
5E ARG* 1.3 84.4 + - - +
6E ASN* 3.4 22.7 - - - +
72E GLN* 3.3 28.9 - - + +
74E ASN* 3.8 10.8 - - - +
182E PRO* 3.5 0.9 - - - +
183E PRO* 3.2 24.0 - - + +
251E LYS* 5.9 0.9 - - + -
252E CYS 3.9 16.6 - - - +
253E GLY* 3.6 12.8 - - - +
254E GLU* 3.8 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 5 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LYS 3.0 26.4 + - - -
3E ASN 4.2 0.4 - - - +
4E ILE* 1.3 103.3 + - - +
6E ASN* 1.3 63.2 + - - +
7E PHE* 3.7 3.4 - - + -
71E TYR* 3.8 11.4 + - + -
72E GLN 2.8 9.2 + - - +
73E LEU* 3.6 26.8 - - + -
74E ASN 2.9 26.9 + - - +
176E LEU* 3.9 13.0 - - + -
177E VAL* 3.1 51.8 + - + +
180E ILE* 3.1 33.8 + - + -
181E PRO 4.6 1.3 - - - -
182E PRO* 3.5 18.2 - - - +
183E PRO* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 6 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E ILE* 3.4 9.3 - - - +
5E ARG* 1.3 71.6 - - - +
7E PHE* 1.3 62.1 + - - +
74E ASN* 3.3 28.1 - - + +
76E ILE* 5.2 0.2 - - + -
94E ALA 3.6 17.3 - - - +
95E CYS* 3.9 3.1 - - - -
96E GLU* 2.9 49.4 + - - +
97E GLY 3.3 6.2 + - - -
180E ILE* 4.1 3.9 - - - +
183E PRO* 3.9 7.5 - - - +
211E ARG* 3.3 17.3 - - - +
253E GLY 3.0 27.9 + - - +
255E VAL* 4.1 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 7 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ARG 3.7 11.4 - - - -
6E ASN* 1.3 75.6 - - - +
8E SER* 1.3 73.8 + - - +
9E ILE* 4.2 6.5 - - + -
24E ILE* 4.8 9.2 - - + -
73E LEU* 4.0 28.0 - - + -
74E ASN 3.1 6.4 + - - +
75E PHE* 2.9 56.4 - + + -
76E ILE* 2.9 6.6 + - - +
95E CYS* 3.6 7.5 - - - +
97E GLY 3.2 19.3 - - - +
98E ALA* 4.3 0.7 - - - +
99E LEU* 3.7 27.8 - - + -
176E LEU* 3.7 33.0 - - + -
180E ILE* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 8 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PHE* 1.3 78.3 - - - +
9E ILE* 1.3 69.0 + - - +
10E ILE* 5.0 1.0 - - - +
76E ILE* 3.3 21.1 - - - +
78E THR* 3.3 14.3 + - - -
91E SER* 5.5 2.7 - - - -
92E LEU* 3.4 26.4 - - - +
95E CYS* 3.7 11.1 - - - -
97E GLY 3.4 5.7 + - - -
98E ALA* 3.5 11.0 - - - +
99E LEU 3.0 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PHE* 4.2 13.0 - - + -
8E SER* 1.3 83.1 - - - +
10E ILE* 1.3 67.2 + - - +
11E ALA* 4.1 8.0 + - + -
20E LEU* 4.9 4.7 - - + -
21E SER* 4.2 25.8 - - - +
24E ILE* 4.4 8.5 - - + -
75E PHE* 4.0 28.0 - - + -
76E ILE 3.5 6.2 + - - +
77E ASP* 4.9 3.9 - - - +
78E THR* 3.4 23.6 + - - +
99E LEU* 3.6 21.8 - - + -
101E VAL* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E SER* 5.0 1.1 - - - +
9E ILE* 1.3 76.8 - - - +
11E ALA* 1.3 61.6 + - - +
78E THR* 4.4 17.7 - - + +
92E LEU* 5.0 4.5 - - + -
98E ALA* 4.3 21.8 - - + -
99E LEU 2.8 15.2 + - - +
100E LEU* 3.6 12.8 - - + +
101E VAL* 2.7 33.1 + - - +
112E THR* 3.7 37.5 - - + +
115E ASN* 4.2 29.2 - - + +
116E CYS* 4.3 13.5 - - + -
119E ALA* 4.4 7.4 - - + -
126E VAL* 6.1 2.2 - - + -
----------------------------------------------------------
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