Contacts of the helix formed by residues 90 - 104 (chain D) in PDB entry 4NH1
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 THR 90 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ARG* 4.1 10.5 - - - +
71B LYS* 5.7 4.9 - - - +
29D TYR* 3.8 24.5 - - + +
86D ARG 3.7 15.7 - - - +
87D TYR* 2.6 25.8 + - - -
89D LEU* 1.3 81.5 - - + +
91D ASN* 1.3 59.3 - - - +
92D ARG* 4.0 4.5 + - - +
93D GLY 3.1 10.7 + - - -
94D ILE* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LYS* 5.7 0.9 + - - -
47B ARG* 4.1 32.5 + - - +
89D LEU 4.0 0.2 + - - -
90D THR* 1.3 73.4 - - - +
92D ARG* 1.3 62.0 + - - +
94D ILE* 4.0 8.1 - - - +
95D ALA* 3.3 22.0 + - - +
170D VAL* 4.4 14.6 - - - +
171D HIS* 5.6 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASP* 3.6 28.8 + - - +
87D TYR* 3.7 13.2 - - + +
90D THR* 3.2 7.0 + - - +
91D ASN* 1.3 77.0 - - - +
93D GLY* 1.3 63.8 + - - +
95D ALA* 3.3 10.5 + - - +
96D GLN* 3.2 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D CYS* 4.8 0.2 - - - -
87D TYR* 3.4 40.7 - - - -
88D ILE* 4.2 7.3 - - - +
90D THR* 3.1 8.1 + - - -
92D ARG* 1.3 79.7 - - - +
94D ILE* 1.3 60.7 + - - +
96D GLN* 3.2 4.6 + - - +
97D MET* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ARG* 4.7 4.9 - - - +
88D ILE 3.3 18.1 + - - +
89D LEU 3.8 16.8 - - - +
90D THR 2.8 19.7 + - - +
91D ASN* 4.0 7.0 - - - +
93D GLY* 1.3 75.4 - - - +
95D ALA* 1.3 53.6 + - - +
97D MET* 3.2 6.7 + - - +
98D LEU* 2.7 34.5 + - + +
163D PHE* 4.8 4.0 - - + -
166D ILE* 4.2 20.6 - - + +
167D LEU* 3.7 28.0 - - + +
170D VAL* 4.0 19.5 - - + -
171D HIS* 3.9 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ASN 3.3 12.7 + - - +
92D ARG* 3.5 15.7 - - - +
93D GLY 3.3 0.2 - - - -
94D ILE* 1.3 79.2 - - - +
96D GLN* 1.3 58.1 + - + +
98D LEU* 3.6 10.4 + - - +
99D GLU* 3.1 25.6 + - - +
171D HIS* 5.2 5.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D CYS* 4.0 17.3 - - + +
24D GLU* 3.0 24.4 + - - +
26D ASP* 2.8 15.1 - - - +
87D TYR* 2.4 32.8 + - - -
92D ARG* 3.2 18.1 + - + +
93D GLY 3.2 7.4 + - - +
94D ILE 3.2 0.6 - - - -
95D ALA* 1.3 76.3 - - + +
97D MET* 1.3 64.9 + - - +
99D GLU* 3.2 8.2 + - - +
100D LYS* 3.1 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PHE 4.0 7.6 - - - +
23D CYS* 3.7 31.2 - - - -
84D HIS* 4.2 7.6 - - + -
88D ILE* 3.7 17.3 - - + -
93D GLY 3.1 15.2 + - - +
94D ILE 3.7 5.4 - - - +
96D GLN* 1.3 72.1 - - - +
98D LEU* 1.3 55.5 + - - +
100D LYS* 3.2 8.9 + - - +
101D TYR* 2.7 33.7 + - - +
106D PHE* 3.6 21.4 - - + -
120D LEU* 5.3 0.7 - - - -
121D PRO* 3.6 31.0 - - + -
159D PHE* 4.7 0.4 - - + -
163D PHE* 3.5 36.6 - - + -
167D LEU* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ILE 2.7 21.2 + - - +
95D ALA* 3.8 8.3 - - - +
97D MET* 1.3 73.2 - - - +
99D GLU* 1.3 56.4 + - - +
101D TYR* 3.3 26.1 - - + +
102D GLN* 3.1 37.1 + - - +
167D LEU* 4.2 26.6 - - + +
171D HIS* 3.6 30.3 - - + +
174D TYR* 3.7 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ALA 3.1 14.2 + - - +
96D GLN* 3.4 11.9 - - - +
97D MET 3.1 0.6 - - - -
98D LEU* 1.3 75.6 - - - +
100D LYS* 1.3 64.7 + - + +
102D GLN* 3.2 32.7 + - - +
103D GLN* 3.3 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLU 3.4 22.9 + - - -
21D PHE 3.9 7.9 - - - +
22D PHE 3.6 14.4 + - - +
23D CYS* 4.1 22.9 - - + -
96D GLN 3.1 14.6 + - - +
97D MET* 3.6 8.3 - - - +
99D GLU* 1.3 74.8 - - + +
101D TYR* 1.3 59.9 + - - +
103D GLN* 3.1 8.7 + - - +
104D GLY 2.8 25.5 + - - -
105D ASP* 2.5 48.0 + - - +
106D PHE* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D MET 2.7 16.4 + - - +
98D LEU* 3.3 28.0 - - + +
99D GLU 3.2 0.2 - - - -
100D LYS* 1.3 78.2 - - - +
102D GLN* 1.3 65.3 + - + +
104D GLY* 3.4 11.4 + - - +
106D PHE* 3.8 7.8 - - - -
117D GLN* 2.9 23.1 + - - -
118D PRO* 3.3 42.6 - - + +
119D MET 3.9 7.4 - - - -
120D LEU* 3.5 37.0 - - + -
138D PRO* 3.8 12.0 - - + +
167D LEU* 6.2 1.1 - - + -
168D PHE* 4.8 5.3 - + - -
174D TYR* 4.4 29.0 + + + -
176D PRO* 4.5 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 3.1 21.2 + - - +
99D GLU* 3.2 31.9 + - - +
100D LYS 3.2 0.2 - - - -
101D TYR* 1.3 85.0 - - + +
103D GLN* 1.3 60.9 + - + +
174D TYR* 3.3 32.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D GLU* 3.3 26.4 + - - +
100D LYS* 3.1 10.0 + - - +
102D GLN* 1.3 78.8 - - + +
104D GLY* 1.3 61.1 + - - +
105D ASP* 3.2 30.7 + - - +
108D TYR* 4.1 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LYS 2.8 5.5 + - - -
101D TYR* 3.4 8.9 + - - -
102D GLN 3.4 2.8 - - - -
103D GLN* 1.3 80.3 - - - +
105D ASP* 1.3 61.7 + - - +
106D PHE* 3.1 8.3 + - - -
107D GLY* 3.4 12.9 + - - -
108D TYR* 4.1 24.9 + - - -
118D PRO* 5.0 3.8 - - - -
----------------------------------------------------------
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