Contacts of the helix formed by residues 96 - 105 (chain D) in PDB entry 4K71
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 PRO 96 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D HIS* 6.0 4.5 - - - +
95D GLU* 1.3 89.7 - - + +
97D GLU* 1.3 82.9 + - + +
98D ARG 3.4 2.2 - - - -
99D ASN* 3.5 5.7 + - + +
100D GLU* 3.4 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LYS* 4.3 23.0 + - + +
94D GLN* 3.1 16.5 + - - +
95D GLU 3.8 3.1 - - - +
96D PRO* 1.3 97.9 - - - +
98D ARG* 1.3 55.1 + - - +
100D GLU* 3.0 10.3 + - - +
101D CYS* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D THR* 3.3 10.3 + - - +
71D GLY* 3.2 18.8 + - - -
72D ASP* 2.9 41.2 + - - +
75D CYS* 3.9 23.5 - - - +
90D CYS 3.4 20.0 - - - +
91D CYS* 4.4 3.1 + - - +
93D LYS* 3.6 21.7 + - - +
94D GLN* 2.8 21.8 + - - +
95D GLU* 2.9 33.7 + - - +
97D GLU* 1.3 75.8 - - - +
99D ASN* 1.3 62.5 + - - +
101D CYS* 3.2 6.9 + - - +
102D PHE* 3.2 38.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.2 27.6 + - - -
67D HIS* 3.1 49.9 + - + +
95D GLU* 3.0 27.6 + - - +
96D PRO 3.9 4.9 - - - +
97D GLU 3.3 0.4 - - - -
98D ARG* 1.3 75.2 - - - +
100D GLU* 1.3 64.5 + - - +
102D PHE* 3.2 18.1 + - - +
103D LEU* 3.2 32.3 + - - +
247D HIS* 4.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D HIS* 5.7 0.3 - - - -
96D PRO* 3.4 15.3 + - + +
97D GLU* 3.0 10.6 + - - +
99D ASN* 1.3 76.8 + - - +
101D CYS* 1.3 65.5 + - - +
103D LEU* 3.4 10.7 + - - +
104D GLN* 3.1 27.1 + - - +
247D HIS* 2.9 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ASP* 4.3 4.3 - - - -
90D CYS* 2.1 54.7 - - + -
93D LYS* 4.2 18.8 - - + +
97D GLU 2.7 16.4 + - - +
98D ARG 3.2 8.9 + - - +
100D GLU* 1.3 73.0 - - - +
102D PHE* 1.3 61.2 + - - +
104D GLN* 3.2 18.1 + - - +
105D HIS* 3.1 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 3.8 33.7 - + + +
31D LEU* 4.8 2.9 - - + -
71D GLY* 5.0 3.8 - - - -
74D LEU* 4.1 32.1 - - + -
75D CYS* 4.0 21.8 - - - -
78D ALA* 4.6 8.1 - - + -
87D MET* 3.6 34.0 - - - +
90D CYS* 3.9 14.4 - - + -
91D CYS* 4.1 4.7 - - - -
98D ARG* 3.2 49.3 + - + -
99D ASN* 3.2 12.0 + - - +
101D CYS* 1.3 74.4 - - - +
103D LEU* 1.3 63.6 + - - +
105D HIS* 3.0 14.0 + - - +
106D LYS* 3.5 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TYR* 4.1 18.4 - - + -
99D ASN* 3.2 26.8 + - - +
100D GLU* 3.7 17.5 - - - +
101D CYS 3.4 0.2 - - - -
102D PHE* 1.3 76.3 - - - +
104D GLN* 1.3 62.6 + - - +
105D HIS 3.4 0.5 + - - -
106D LYS* 3.6 28.7 + - + +
148D TYR* 4.0 8.7 + - - -
246D CYS 4.9 2.9 - - - +
247D HIS* 3.1 65.7 - - + +
248D GLY* 4.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D LYS* 6.0 1.6 - - - +
100D GLU* 3.1 15.4 + - - +
101D CYS* 3.4 16.0 - - - +
103D LEU* 1.3 76.1 - - - +
105D HIS* 1.3 75.6 + - + +
106D LYS 3.6 5.0 + - - +
148D TYR* 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLN* 4.3 0.2 - - - +
86D GLU* 3.5 50.7 + - + +
87D MET* 3.3 35.4 - - + +
89D ASP* 5.2 1.6 - - + -
90D CYS* 3.4 11.5 - - - -
101D CYS* 3.1 35.6 + - - -
102D PHE 3.0 6.8 + - - +
104D GLN* 1.3 90.3 + - + +
106D LYS* 1.3 66.7 + - - +
107D ASP* 3.0 8.7 + - - +
----------------------------------------------------------
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