Contacts of the helix formed by residues 2108 - 2118 (chain A) in PDB entry 5Z58
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 LYS2108 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2090A ILE* 4.1 19.1 - - + +
2106A LEU 3.4 1.3 + - - -
2107A PRO* 1.3 70.6 - - - +
2109A ASN* 1.3 66.2 + - - +
2111A LEU* 3.1 10.6 + - + +
2112A LYS* 2.9 30.4 + - + +
2263A LEU* 3.8 43.7 - - + -
2264A SER* 2.8 17.3 + - - +
2265A ASP* 3.5 35.7 + - - +
2267A PHE 4.8 0.6 + - - -
2268A LEU* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2107A PRO* 4.0 2.4 - - - +
2108A LYS* 1.3 79.7 - - - +
2110A VAL* 1.3 78.3 + - - +
2112A LYS* 3.1 8.7 + - - +
2113A LYS* 3.0 22.1 + - - +
2268A LEU* 3.7 35.5 - - + +
2269A GLY 3.0 38.3 + - - +
1228D VAL* 4.1 15.4 - - - +
1229D ASP* 5.3 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2106A LEU* 3.7 14.8 - - + -
2107A PRO* 3.2 27.4 - - + +
2109A ASN* 1.3 83.8 + - - +
2111A LEU* 1.3 61.0 + - - +
2113A LYS* 3.3 1.0 + - - -
2114A PHE* 2.8 32.8 + - - +
2142A ILE* 5.6 0.9 - - + -
2144A CYS* 5.5 0.9 - - - +
2145A ILE* 3.7 23.6 - - + +
2269A GLY* 3.4 36.6 - - - +
2270A PHE* 3.7 12.3 - - - +
2271A PHE* 3.8 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2090A ILE* 5.1 7.9 - - + -
2106A LEU* 4.1 14.6 - - + -
2107A PRO 4.1 5.4 - - - +
2108A LYS* 3.1 16.8 + - + +
2110A VAL* 1.3 79.8 - - - +
2112A LYS* 1.3 66.9 + - - +
2114A PHE* 3.2 6.1 + - + +
2115A ILE* 2.9 44.8 + - + +
2145A ILE* 5.5 0.9 - - - -
2178A ILE* 4.3 14.6 - - + -
2216A CYS* 4.7 2.0 - - - -
2225A LEU* 3.5 33.2 - - + -
2263A LEU* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2084A HIS* 6.1 1.4 - - - +
2087A THR* 3.1 50.8 + - + +
2108A LYS* 2.9 18.4 + - + +
2109A ASN* 3.4 11.4 - - - +
2111A LEU* 1.3 78.4 - - + +
2113A LYS* 1.3 64.9 + - - +
2115A ILE* 3.0 6.3 + - - +
2116A CYS* 2.9 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2109A ASN 3.0 9.8 + - - +
2110A VAL* 3.9 1.6 - - - +
2112A LYS* 1.3 77.9 - - - +
2114A PHE* 1.3 58.3 + - - +
2116A CYS* 3.1 10.2 + - + +
2117A ILE* 3.0 39.1 + - + +
2271A PHE* 3.7 24.5 - - + -
2300A ASN* 3.9 3.1 - - + -
2301A PRO* 3.8 27.8 + - + +
1229D ASP* 2.2 62.2 + - + +
1230D SER 4.6 3.8 + - - -
1231D GLU* 4.9 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2110A VAL 2.8 19.3 + - - +
2111A LEU* 3.6 9.6 - - + +
2113A LYS* 1.3 77.7 - - - +
2115A ILE* 1.3 64.8 + - + +
2117A ILE* 3.3 19.3 - - - +
2118A SER* 3.6 9.7 + - - -
2124A ILE* 3.6 30.9 - - + +
2125A ALA 4.0 0.7 - - - -
2126A GLY* 3.9 19.5 - - - -
2145A ILE* 4.7 5.8 - - + -
2147A MET* 3.9 21.5 - - + -
2178A ILE* 3.5 51.6 - - + -
2179A HIS 4.4 0.4 - - - -
2180A THR* 3.6 24.7 - - + -
2216A CYS* 5.0 2.7 - - + -
2271A PHE* 4.1 13.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2083A LEU* 3.6 28.3 - - + +
2086A ARG* 4.4 9.0 - - + -
2087A THR* 4.9 9.4 - - - +
2090A ILE* 4.6 8.7 - - + -
2111A LEU* 2.9 39.9 + - + +
2112A LYS* 3.5 9.0 - - - +
2114A PHE* 1.3 79.6 - - + +
2116A CYS* 1.3 62.4 + - - +
2118A SER* 2.9 23.8 + - - -
2180A THR* 5.4 1.1 - - + -
2216A CYS* 3.9 12.3 - - - -
2218A PHE* 4.2 17.0 - - + -
2223A CYS* 3.6 31.4 - - + -
2225A LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS2116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2080A ALA 4.9 2.3 - - - +
2083A LEU* 3.9 17.2 - - + +
2084A HIS* 3.7 36.6 - - - -
2087A THR* 4.2 8.3 - - - -
2112A LYS* 2.9 23.7 + - - +
2113A LYS* 3.1 15.2 + - + +
2115A ILE* 1.3 80.0 - - - +
2117A ILE* 1.3 62.5 + - + +
2118A SER 3.5 0.2 + - - -
2303A GLU* 4.7 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2113A LYS* 3.0 22.5 + - + +
2114A PHE* 3.3 22.2 - - + +
2116A CYS* 1.3 74.8 - - + +
2118A SER* 1.3 66.4 + - - +
2124A ILE* 4.0 9.6 - - + -
2147A MET* 3.6 19.3 - - + -
2271A PHE* 4.7 0.7 - - + -
2279A TRP* 3.9 4.8 - - + -
2301A PRO* 3.4 37.0 - - + +
2302A LYS 3.4 31.9 - - - +
2303A GLU* 3.8 8.7 - - + +
2304A PHE* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2080A ALA* 4.2 4.2 - - - +
2083A LEU* 3.0 17.9 - - - +
2114A PHE 3.8 2.2 - - - -
2115A ILE 2.9 17.9 + - - -
2116A CYS 3.3 1.6 - - - +
2117A ILE* 1.3 84.8 - - - +
2119A ASP* 1.3 66.6 + - - +
2124A ILE* 3.7 26.7 - - - -
2180A THR* 3.7 19.7 - - - -
2218A PHE* 3.1 21.5 - - - -
2304A PHE* 3.8 7.7 - - - +
----------------------------------------------------------
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