Contacts of the strand formed by residues 53 - 59 (chain B) in PDB entry 2JG1
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 53 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 3.6 3.0 - - - +
2B ILE* 3.3 12.8 - - + +
4B THR* 3.9 26.9 - - + -
43B THR* 4.3 28.3 - - + +
46B LEU* 4.0 20.4 - - + -
47B ALA* 4.5 11.0 - - + +
51B GLU 3.3 12.3 + - - +
52B PRO* 1.3 74.6 - - - +
54B LEU* 1.3 67.3 + - - +
76B ILE* 4.9 6.3 - - + -
77B LYS* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 4.1 15.0 - - + -
2B ILE 2.8 10.6 + - - +
3B LEU* 3.4 14.7 - - + +
4B THR* 3.0 24.4 + - - -
53B VAL* 1.3 79.1 - - - +
55B ALA* 1.3 62.9 + - - +
77B LYS* 3.6 14.4 - - + -
78B HIS* 3.6 39.0 - - - +
79B ALA* 4.1 8.1 - - + +
124B MSE 3.9 28.9 - - + -
127B LYS* 6.1 5.2 - - + -
128B VAL* 5.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 3.5 14.1 - - - +
40B LEU* 4.2 10.3 - - + -
43B THR* 4.2 17.0 - - + +
53B VAL 4.3 0.2 - - - -
54B LEU* 1.3 73.1 - - - +
56B SER* 1.3 61.0 + - - +
71B LEU* 4.3 4.0 - - + -
76B ILE* 4.8 0.2 - - + -
77B LYS 2.9 16.3 + - - +
78B HIS* 3.2 5.8 - - + +
79B ALA 2.8 27.2 + - - -
80B PHE* 4.0 20.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.8 19.7 - - - -
4B THR 2.9 11.5 + - - +
5B LEU* 4.1 8.3 - - - -
6B THR* 3.0 22.2 + - - -
55B ALA* 1.3 73.4 - - - +
57B GLY* 1.3 64.0 + - - +
79B ALA* 2.6 26.5 + - - -
80B PHE* 3.4 18.4 - - - -
117B PHE* 3.6 8.5 - - - -
120B HIS* 3.9 0.9 + - - -
124B MSE 3.6 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR 3.3 15.5 - - - -
7B LEU* 3.9 14.4 - - - -
56B SER* 1.3 83.0 + - - +
58B PHE* 1.3 59.5 + - - -
80B PHE* 3.4 4.8 - - - -
81B TYR* 2.8 34.8 + - - +
117B PHE* 3.9 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR 3.5 5.7 + - - -
7B LEU* 3.5 42.8 - - + +
9B PRO* 3.1 28.8 - - - +
57B GLY* 1.3 72.6 - - - -
59B ILE* 1.3 61.7 + - - +
80B PHE* 4.4 0.2 - - - -
81B TYR* 3.4 15.0 - + + -
83B ILE* 3.5 28.0 - - + -
87B THR* 4.5 0.3 + - - -
107B PRO* 6.4 0.2 - - + -
109B ILE* 4.0 34.1 - - + -
113B GLU 3.9 10.5 - - - -
114B ALA* 4.7 0.2 - - - -
117B PHE* 3.5 35.4 - + + -
138B PRO* 4.4 0.4 - - + -
141B LEU* 4.1 20.4 - - + -
145B TYR* 3.8 12.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 4.0 13.2 - - + -
58B PHE* 1.3 80.4 - - - +
60B GLY* 1.3 58.6 + - - +
64B GLY* 3.8 28.9 - - - +
65B GLN* 5.6 0.2 - - - -
67B ILE* 4.3 13.0 - - + -
68B ALA* 4.8 12.1 - - + +
78B HIS* 5.8 1.3 - - + +
80B PHE* 3.5 43.1 - - + -
81B TYR 3.0 9.0 + - - +
82B ASN* 3.2 28.7 - - - +
83B ILE* 2.9 27.6 + - - -
87B THR* 3.5 6.7 - - - +
----------------------------------------------------------
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