Contacts of the strand formed by residues 50 - 54 (chain G) in PDB entry 1PV2
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 LYS 50 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G LYS 3.9 10.3 + - - +
49G HIS* 1.3 75.0 - - - +
51G ILE* 1.3 65.2 + - - +
52G LEU 4.0 0.2 - - - -
90G PHE* 5.5 0.2 - - - -
91G GLU* 3.3 36.1 - - + +
92G PHE* 4.4 7.0 - - - +
93G GLU* 3.1 28.7 + - - +
145G GLU* 2.7 13.6 + - + +
146G TYR* 3.2 18.4 - - + -
147G ALA* 2.8 26.1 + - - -
148G ALA 3.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G LYS* 1.3 75.5 - - - +
52G LEU* 1.3 63.6 + - - +
53G VAL* 3.3 8.4 + - + -
82G LEU* 4.1 9.6 - - + -
85G LEU* 3.6 47.8 - - + -
90G PHE* 3.7 20.9 - - + +
91G GLU 2.8 14.8 + - - +
92G PHE* 3.3 4.4 - - + +
93G GLU 2.9 26.9 + - - +
146G TYR* 4.2 1.3 - - - -
148G ALA* 3.7 24.0 - - + +
150G PHE* 3.9 28.5 - - + -
182G ILE* 5.5 0.2 - - + -
277G MET* 4.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 1.3 70.9 - - - +
53G VAL* 1.3 59.3 + - - +
54G ILE* 3.9 6.0 + - + -
93G GLU* 3.6 11.4 - - + +
94G VAL 4.7 0.2 - - - -
95G ALA* 4.0 24.7 - - + +
131G LYS* 6.5 0.2 - - + -
133G LEU* 4.4 13.0 - - + -
136G VAL* 3.9 23.8 - - + -
140G LEU* 5.2 6.5 - - + -
146G TYR* 3.6 38.1 - - + +
148G ALA 2.9 14.4 + - - +
149G ILE* 3.3 25.0 - - + +
150G PHE 2.6 33.4 + - - +
170G ALA* 5.3 2.7 - - + -
173G TRP* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 3.9 14.8 - - + +
52G LEU* 1.3 77.2 - - - +
54G ILE* 1.3 65.5 + - - +
55G ALA* 3.7 5.9 + - + +
78G THR* 5.5 0.2 - - - +
82G LEU* 3.9 34.5 - - + -
92G PHE* 4.1 5.8 - - + -
93G GLU 2.8 15.8 + - - +
94G VAL* 3.4 14.1 - - + +
95G ALA* 2.9 28.8 + - - +
127G PHE* 4.7 7.6 - - + -
150G PHE* 3.4 10.3 - - + +
152G PRO* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G LEU* 3.9 6.3 + - + -
53G VAL* 1.3 71.9 - - - +
55G ALA* 1.3 65.5 + - - +
73G ASN* 5.4 0.2 + - - -
95G ALA 3.3 7.2 - - - +
96G THR* 5.4 1.6 - - - -
97G ILE* 5.4 0.7 - - + -
133G LEU* 3.7 35.9 - - + -
149G ILE* 4.1 23.6 - - + -
150G PHE 2.9 13.0 + - - +
151G VAL* 4.0 18.3 - - + +
152G PRO* 3.4 20.1 - - - +
161G LEU* 3.9 17.9 - - + +
167G VAL* 3.9 31.0 - - + +
170G ALA* 4.5 14.1 - - + -
171G LEU* 5.6 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