Contacts of the strand formed by residues 60 - 66 (chain A) in PDB entry 2EBJ
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 ALA 60 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.0 1.8 + - - -
2A ILE* 3.0 18.3 - - + +
3A LEU 2.9 24.3 + - - -
58A PRO* 3.2 3.2 + - - +
59A LYS* 1.3 83.5 - - + +
61A VAL* 1.3 68.4 + - - +
154A VAL* 4.0 1.8 - - - -
155A PRO* 3.5 22.4 - - + +
192A LEU* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 4.3 1.8 - - - -
3A LEU* 3.4 21.5 - - + +
5A THR* 5.2 0.2 - - + -
54A HIS* 5.3 0.7 - - + +
58A PRO* 3.9 18.8 - - + -
60A ALA* 1.3 83.4 - - - +
62A LEU* 1.3 64.2 + - - +
63A HIS* 3.6 39.9 - - + +
112A PHE* 5.2 0.9 - - - -
146A SER* 4.7 1.3 - - - +
150A LEU* 3.7 26.7 - - + -
154A VAL* 4.5 1.3 - - + -
155A PRO 2.8 13.1 + - - +
156A VAL* 3.3 10.1 - - + -
157A GLY 3.0 24.3 + - - -
192A LEU* 4.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 4.2 0.2 - - - +
3A LEU 2.9 11.5 + - - +
4A VAL* 3.3 7.5 - - + +
5A THR 3.1 22.5 + - - -
61A VAL* 1.3 74.3 - - - +
63A HIS* 1.3 64.5 + - - +
64A LEU* 4.1 12.6 - - + -
75A LEU* 5.2 0.9 - - + -
112A PHE* 4.1 22.4 - - + -
157A GLY* 3.6 22.0 - - - +
158A PHE 4.1 2.7 - - - +
159A LEU* 4.4 12.6 - - + +
185A VAL* 4.2 16.8 - - + -
188A ALA* 4.3 15.9 - - + -
189A LEU* 3.6 38.1 - - + +
192A LEU* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.9 1.8 - - + -
5A THR* 2.7 31.3 + - + +
7A PHE* 5.9 0.9 - - + -
39A LEU* 4.3 6.1 - - + +
50A LEU* 3.7 20.6 - - + -
61A VAL* 3.6 22.2 - - + +
62A LEU* 1.3 73.5 - - - +
64A LEU* 1.3 63.0 + - - +
142A ALA* 3.8 21.7 + - + -
143A PHE* 4.3 5.6 - - - -
146A SER* 2.8 34.0 + - - -
156A VAL* 4.4 3.6 - - + -
157A GLY 3.0 13.0 + - - +
158A PHE* 3.2 26.9 - + + -
159A LEU 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 4.1 17.7 - - + -
5A THR* 2.9 26.9 + - - +
6A GLY* 3.8 4.5 - - - -
7A PHE* 3.5 21.1 - - - -
18A SER* 3.9 16.2 - - - +
21A LEU* 3.9 32.5 - - + -
22A LEU* 4.3 6.7 - - + -
62A LEU* 4.1 14.8 - - + +
63A HIS* 1.3 76.6 - - - +
65A GLY* 1.3 59.4 + - - +
158A PHE* 3.7 3.8 - - - -
159A LEU* 3.4 32.1 - - + +
161A LEU* 4.3 4.7 - - + -
185A VAL* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 4.3 2.7 - - - -
18A SER* 3.8 13.0 - - - -
64A LEU* 1.3 77.4 - - - +
66A LEU* 1.3 61.6 + - - -
139A CYS* 3.8 19.7 - - - -
158A PHE* 3.7 4.5 - - - -
159A LEU 3.3 5.5 + - - -
160A HIS* 3.4 7.0 - - - -
161A LEU* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 4.3 22.8 - - + -
13A LEU* 5.7 3.8 - - + -
15A HIS 4.9 4.5 - - - +
16A ASN* 3.8 25.3 + - - +
17A PRO* 4.0 15.7 - - + -
18A SER* 5.3 1.1 - - - +
65A GLY* 1.3 71.9 - - - -
67A ALA* 1.3 62.5 + - - +
68A GLU* 3.5 38.2 + - + +
139A CYS* 4.4 7.2 - - - -
160A HIS* 3.7 8.6 + - - -
161A LEU* 3.3 19.3 - - - +
162A PRO 3.8 18.2 - - - +
163A PRO* 4.0 9.6 - - + -
167A LEU* 3.9 17.3 - - + -
----------------------------------------------------------
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