Contacts of the strand formed by residues 2073 - 2078 (chain B) in PDB entry 5G1N
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 MET2073 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2063B ILE* 5.0 1.1 - - + -
2067B LEU* 3.3 52.9 - - + +
2069B THR* 3.5 17.7 - - - +
2070B VAL* 3.0 32.7 + - + +
2071B ASN 4.8 2.9 - - - +
2072B GLY* 1.3 83.8 - - - +
2074B THR* 1.3 62.1 + - - +
2075B ILE* 4.0 9.9 - - + -
2098B ARG 3.9 0.8 + - - -
2099B VAL* 3.4 10.2 - - + +
2100B SER* 3.3 23.7 + - - -
2140B ASP* 3.6 24.0 - - + +
2141B VAL* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR2074 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2073B MET* 1.3 70.1 - - - +
2075B ILE* 1.3 62.7 + - - +
2076B THR* 4.4 2.5 - - - +
2100B SER* 2.7 27.9 + - - +
2102B ARG* 3.8 36.6 + - + +
2138B ASP* 3.4 25.6 + - - +
2139B THR* 3.7 7.6 - - - -
2140B ASP* 2.8 36.6 + - - -
2141B VAL 3.2 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2075 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2063B ILE* 4.6 7.2 - - + -
2070B VAL* 5.2 1.8 - - + -
2073B MET* 4.2 6.5 - - + +
2074B THR* 1.3 75.0 - - - +
2076B THR* 1.3 60.6 + - - +
2077B MET* 4.0 27.2 + - + +
2090B LEU* 5.3 2.7 - - + -
2094B LEU* 3.8 23.8 - - + -
2099B VAL* 3.4 42.2 - - + -
2100B SER 3.2 3.0 + - - -
2101B LEU* 3.5 14.0 - - + +
2102B ARG 3.0 23.8 + - - +
2141B VAL* 3.3 36.3 - - + +
2143B TYR* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR2076 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2074B THR* 3.8 1.3 + - - +
2075B ILE* 1.3 71.2 - - - +
2077B MET* 1.3 56.8 + - - +
2078B VAL* 3.7 9.0 - - + -
2102B ARG* 3.2 26.8 - - + +
2104B VAL* 3.6 28.7 - - + -
2132B ILE* 6.1 0.7 - - - -
2135B ALA* 4.1 11.6 - - + +
2136B LEU* 6.2 0.4 - - + -
2139B THR* 2.6 33.5 + - - +
2141B VAL 2.7 8.9 + - - -
2142B LEU* 3.5 10.6 - - + +
2143B TYR* 2.7 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET2077 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2075B ILE* 4.2 16.8 - - + +
2076B THR* 1.3 71.0 - - - +
2078B VAL* 1.3 57.8 + - - +
2081B LEU* 4.0 14.1 - - + +
2087B VAL* 4.2 14.8 - - + +
2090B LEU* 4.1 22.0 - - + -
2091B ALA* 4.0 28.5 - - - +
2094B LEU* 4.3 7.0 - - + -
2101B LEU* 4.5 9.9 - - + -
2102B ARG 2.7 12.7 + - - +
2103B TYR* 3.4 29.7 - - + -
2104B VAL 2.7 32.2 + - - +
2111B MET* 3.8 13.2 - - - -
2143B TYR* 3.4 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2078 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2076B THR* 3.7 7.4 - - + +
2077B MET* 1.3 78.1 - - - +
2079B GLY* 1.3 61.9 + - - +
2081B LEU* 4.2 3.7 - - - +
2104B VAL* 3.2 29.8 - - + +
2132B ILE* 4.1 12.6 - - + -
2142B LEU* 3.4 31.4 - - + -
2143B TYR 2.8 9.6 + - - +
2144B MET* 3.8 17.1 - - + +
2145B THR* 2.8 34.9 + - - +
2165B PHE* 3.7 27.1 - - + -
----------------------------------------------------------
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