Contacts of the helix formed by residues 91 - 100 (chain L) in PDB entry 5NSS
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 ARG 91 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L HIS* 3.9 24.0 - - + -
81L GLU 5.3 2.7 - - - +
88L ALA* 4.2 10.0 + - + +
90L LYS* 1.3 81.6 - - - +
92L HIS* 1.3 65.4 + - - +
94L GLY* 3.1 10.2 + - - -
95L ARG* 3.7 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L GLU* 5.0 8.6 + - - +
79L GLY* 3.7 30.3 - - - -
80L HIS* 3.9 9.4 + - - +
90L LYS 3.1 1.0 + - - -
91L ARG* 1.3 78.8 - - - +
93L PRO* 1.3 62.6 - - - +
95L ARG* 3.1 17.3 + - - +
96L PHE* 3.3 10.9 + - - +
129L LEU* 5.2 13.2 - - + +
130L GLU 4.7 5.8 - - - +
131L ARG* 5.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 93 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L GLN 3.3 26.0 - - - +
90L LYS* 3.1 4.3 - - - +
92L HIS* 1.3 77.0 - - - +
94L GLY* 1.3 59.3 + - - +
96L PHE* 3.5 19.3 + - + +
97L GLU* 4.4 4.3 + - - +
138L LEU* 5.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L LYS* 4.0 10.5 + - - +
91L ARG 3.1 11.9 + - - -
93L PRO* 1.3 79.3 - - - +
95L ARG* 1.3 58.1 + - - +
96L PHE 3.4 0.6 + - - -
97L GLU* 4.3 7.7 + - - +
98L ARG* 4.4 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L GLU 5.9 2.7 - - - +
91L ARG 3.7 6.6 + - - +
92L HIS* 3.1 11.6 + - - +
94L GLY* 1.3 75.0 - - - +
96L PHE* 1.3 63.1 + - - +
97L GLU 3.4 1.1 - - - -
98L ARG* 3.6 11.3 + - + +
99L ALA* 3.4 21.0 + - - +
140L VAL* 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92L HIS 3.3 10.1 + - - +
93L PRO* 3.7 14.4 - - + +
94L GLY 3.4 1.2 - - - -
95L ARG* 1.3 77.4 - - - +
97L GLU* 1.3 62.5 + - - +
99L ALA* 3.4 11.4 + - - +
100L ASP* 3.7 11.3 + - - +
129L LEU* 5.6 3.1 - - + -
138L LEU* 4.3 24.5 - - + -
139L GLN 4.5 5.6 - - - +
140L VAL* 4.2 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L PRO* 5.0 2.4 - - - +
93L PRO 4.4 3.8 + - - +
94L GLY 4.3 6.7 + - - +
96L PHE* 1.3 78.8 - - - +
98L ARG* 1.3 61.8 + - - +
99L ALA 3.3 0.2 - - - -
100L ASP* 3.4 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L PRO* 3.8 35.9 - - + +
60L PHE 5.8 0.4 - - - -
61L ILE* 4.3 22.9 - - + +
94L GLY 4.4 5.0 + - - +
95L ARG* 3.6 18.0 + - + +
96L PHE 3.2 1.0 - - - -
97L GLU* 1.3 78.1 - - - +
99L ALA* 1.3 63.2 + - - +
100L ASP 4.1 2.5 - - - +
102L GLY* 4.5 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L ILE* 5.4 4.7 - - - -
95L ARG 3.4 11.0 + - - +
96L PHE 3.7 9.4 - - - +
97L GLU 3.3 1.0 - - - -
98L ARG* 1.3 76.6 - - - +
100L ASP* 1.3 65.3 + - - +
102L GLY 3.2 20.8 + - - +
103L THR 6.2 0.2 - - - -
140L VAL* 3.8 20.9 - - + -
141L ASN 2.9 15.0 - - - +
142L VAL* 3.3 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L PRO* 5.3 3.6 - - - +
96L PHE 3.7 8.8 + - - +
97L GLU* 3.4 19.6 + - - +
98L ARG 3.5 1.8 - - - +
99L ALA* 1.3 78.0 - - - +
101L GLY* 1.3 61.3 + - - +
102L GLY 3.7 0.2 + - - -
139L GLN 5.7 3.4 - - - +
141L ASN* 3.5 14.7 + - + +
----------------------------------------------------------
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