Contacts of the strand formed by residues 67 - 71 (chain 2) in PDB entry 1JJ2
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 LEU 67 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24570 U 5.5 3.9 + - - -
32 MET* 4.1 10.5 - - - -
222 VAL* 3.9 16.6 - - + -
232 GLU 3.4 11.2 - - - +
242 LYS* 3.8 8.5 - - + -
252 VAL* 3.8 6.3 - - - +
652 THR* 3.1 31.7 + - + +
662 ASP* 1.3 82.1 + - - +
682 LYS* 1.3 61.4 + - - +
692 TYR* 3.6 33.7 - - + +
792 LEU* 3.5 21.1 - - - +
802 ARG 4.7 3.3 + - - +
832 TRP* 4.2 0.7 - - + -
882 LEU* 3.7 27.1 - - + -
902 PHE* 3.8 16.2 - - + -
85042 CL 3.9 2.0 - - + -
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Residues in contact with LYS 68 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24350 U 3.0 33.2 + - - +
24360 U 2.8 31.6 + - - +
212 GLU 3.4 1.9 - - - +
222 VAL* 3.4 7.4 - - - +
232 GLU* 2.8 57.8 + - + +
252 VAL* 3.7 29.6 - - + +
262 ARG* 5.1 4.8 + - - +
672 LEU* 1.3 72.6 - - - +
692 TYR* 1.3 62.1 + - - +
702 ARG* 3.9 20.0 - - + +
772 ALA* 4.8 6.5 - - + -
782 HIS 4.1 3.8 - - - -
792 LEU* 4.3 6.3 - - + -
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Residues in contact with TYR 69 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32 MET* 4.4 5.4 - - + +
72 PHE* 3.9 20.4 - + - -
92 THR* 5.4 0.4 - - + -
202 HIS* 4.0 8.7 - - + -
212 GLU 3.6 3.8 - - - -
222 VAL* 3.9 21.1 - - + -
652 THR* 4.7 1.0 - - - +
672 LEU* 3.6 40.2 - - + +
682 LYS* 1.3 73.2 - - - +
702 ARG* 1.3 61.7 + - - +
712 CYS 4.0 0.3 + - - -
772 ALA* 3.0 2.3 - - - -
782 HIS* 2.9 64.4 + + + +
802 ARG* 3.6 58.1 + - + +
812 GLU 5.0 0.5 + - - -
832 TRP* 3.9 17.5 - - - -
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Residues in contact with ARG 70 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24360 U 3.8 20.8 + - - -
24370 A 3.9 9.9 + - - -
202 HIS* 3.1 4.3 - - - -
212 GLU* 2.8 58.0 + - + +
232 GLU* 4.3 18.2 + - + -
682 LYS* 4.2 15.7 - - + +
692 TYR* 1.3 72.1 - - - +
712 CYS* 1.3 69.0 + - - +
722 GLY 3.4 0.5 + - - -
752 GLY 3.2 24.6 + - - +
772 ALA* 3.4 28.7 - - + +
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Residues in contact with CYS 71 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112 CYS* 3.9 11.4 - - - -
182 GLN* 3.8 24.7 - - - -
192 GLU 4.0 0.4 - - - -
202 HIS* 3.6 14.3 - - - +
702 ARG* 1.3 73.7 - - - +
722 GLY* 1.3 62.6 + - - +
732 GLU 3.5 12.8 - - - -
742 CYS* 3.6 10.3 - - - -
752 GLY* 3.2 23.0 + - - -
762 LYS 3.1 21.3 + - - +
84042 CD 2.4 30.5 - - - -
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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
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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) + - + + + + + -
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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