Contacts of the strand formed by residues 2238 - 2245 (chain A) in PDB entry 4NF9
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 GLU2238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2171A LEU* 6.3 0.2 - - - -
2233A ASP 3.6 1.2 - - - +
2234A ILE* 3.4 8.3 - - - +
2235A ASN* 2.9 45.7 + - - +
2236A ASN 4.4 3.6 - - - +
2237A ASN* 1.3 81.2 - - - +
2239A LEU* 1.3 61.9 + - - +
2240A ARG* 2.9 39.5 + - - +
2255A THR* 4.0 8.3 - - + -
2256A LEU 3.5 2.0 - - - -
2257A PHE* 3.1 42.8 - - + -
2258A LEU* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2171A LEU* 5.2 0.4 - - + -
2217A ILE* 4.0 13.9 - - + -
2232A ILE* 4.1 12.3 - - + -
2233A ASP 3.6 0.2 - - - -
2234A ILE* 3.4 31.4 - - + -
2238A GLU* 1.3 73.3 - - - +
2240A ARG* 1.3 61.1 + - - +
2241A LEU* 3.8 13.5 + - + +
2254A ILE 3.4 2.3 - - - +
2255A THR* 3.2 3.7 - - - -
2256A LEU* 2.7 53.1 + - + +
2258A LEU* 3.8 25.6 - - + -
2297A LEU* 3.5 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2231A ASN* 3.7 2.8 + - - +
2232A ILE* 3.3 6.9 - - - -
2233A ASP* 2.6 64.8 + - + +
2235A ASN* 3.7 25.5 - - - +
2238A GLU* 2.9 37.0 + - - +
2239A LEU* 1.3 74.4 - - - +
2241A LEU* 1.3 63.8 + - - +
2242A LEU 4.0 0.2 + - - -
2253A GLU* 3.8 28.5 + - - +
2254A ILE 3.5 4.0 - - - -
2255A THR* 3.7 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2220A LEU* 5.3 2.7 - - + -
2229A LEU* 3.5 14.8 - - + -
2231A ASN 3.8 1.1 - - - -
2232A ILE* 3.6 35.7 - - + -
2239A LEU* 4.3 14.1 - - + +
2240A ARG* 1.3 76.4 - - - +
2242A LEU* 1.3 60.2 + - - +
2243A PHE* 4.0 4.9 + - + -
2252A PHE 3.8 0.9 - - - +
2253A GLU* 3.1 6.8 - - - -
2254A ILE* 2.7 61.5 + - + +
2256A LEU* 3.9 26.9 - - + -
2297A LEU* 4.8 4.9 - - + -
2300A VAL* 5.3 2.5 - - + -
2301A VAL* 4.0 25.1 - - + -
2304A ILE* 5.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2229A LEU* 3.5 2.5 - - - +
2230A MSE 2.6 46.6 + - + -
2231A ASN* 3.0 39.9 + - + +
2240A ARG 4.0 0.6 + - - -
2241A LEU* 1.3 71.4 - - - +
2243A PHE* 1.3 61.8 + - - +
2244A SER* 5.1 2.9 - - - -
2251A LYS* 4.3 17.5 - - + -
2252A PHE 3.6 14.4 - - - +
2253A GLU* 4.5 12.1 - - + +
2274A HIS* 4.0 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2227A TYR 3.7 20.6 - - - -
2228A ASN* 3.3 15.7 - - + -
2229A LEU* 3.6 32.1 - - + -
2241A LEU* 4.0 1.8 - - + -
2242A LEU* 1.3 72.1 - - - +
2244A SER* 1.3 61.5 + - - +
2251A LYS* 3.1 9.7 - - - +
2252A PHE* 3.0 59.0 + + + +
2254A ILE* 3.8 23.6 - - + -
2301A VAL* 4.3 23.1 - - + -
2304A ILE* 3.7 33.9 - - + -
2309A PHE* 3.6 19.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2228A ASN* 3.0 21.4 + - - +
2230A MSE 3.6 30.4 - - - +
2242A LEU* 4.0 4.9 + - - -
2243A PHE* 1.3 73.2 - - - +
2245A SER* 1.3 63.6 + - - +
2246A SER 5.3 0.3 + - - -
2250A ALA 3.6 3.8 - - - -
2251A LYS* 3.4 26.1 - - - +
2309A PHE* 4.1 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2228A ASN* 4.1 9.8 + - - -
2244A SER* 1.3 76.2 + - - +
2246A SER* 1.3 65.0 + - - +
2247A ALA* 3.3 12.6 + - - +
2248A ALA* 3.1 18.2 + - - +
2249A PHE 2.9 16.5 + - - -
2250A ALA 2.9 24.1 + - - -
2275A VAL* 6.4 0.2 - - - -
2309A PHE* 3.5 25.7 - - - -
----------------------------------------------------------
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