Contacts of the helix formed by residues 78 - 90 (chain A) in PDB entry 2NSG
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 SER 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 3.2 8.6 - - - +
77A VAL* 1.3 84.3 - - - +
79A PRO* 1.3 77.3 - - - +
80A GLU* 3.6 13.9 + - - +
81A ALA* 3.1 23.2 + - - +
82A ARG* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 1.3 88.7 - - - +
80A GLU* 1.3 79.2 + - - +
82A ARG* 3.2 9.8 - - + +
83A ASN* 3.2 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 3.6 11.5 + - - +
79A PRO* 1.3 97.2 - - - +
81A ALA* 1.3 66.4 + - - +
82A ARG 3.1 0.3 + - - -
83A ASN* 3.1 8.8 + - - +
84A GLU* 2.9 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.7 30.1 - - + +
78A SER* 3.1 17.3 + - - +
80A GLU* 1.3 78.3 - - - +
82A ARG* 1.3 62.6 + - - +
84A GLU* 3.8 11.0 - - - +
85A GLU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 6.0 0.4 - - - -
52A ALA 5.1 2.8 + - - -
55A TYR* 6.0 0.8 - - - +
76A TYR* 3.2 62.8 + - + +
77A VAL 5.7 0.2 - - - +
78A SER 3.0 13.0 + - - +
79A PRO* 3.2 13.0 - - + +
80A GLU 3.1 0.2 - - - -
81A ALA* 1.3 78.1 - - - +
83A ASN* 1.3 75.3 + - - +
85A GLU* 3.1 12.3 + - - +
86A ILE* 3.1 34.7 + - + +
127A ALA* 5.6 2.0 - - - +
128A GLN* 5.8 1.6 + - - -
301A GOL 3.7 26.9 + - - -
403A SO4 2.8 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 3.2 17.9 + - - +
80A GLU* 3.1 9.1 + - - +
82A ARG* 1.3 90.7 + - - +
84A GLU* 1.3 58.6 + - + +
86A ILE* 3.2 12.8 + - - +
87A ALA* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 2.9 36.4 + - - +
81A ALA* 3.8 8.6 - - - +
83A ASN* 1.3 77.1 - - + +
85A GLU* 1.3 59.2 + - - +
87A ALA* 3.5 7.9 + - - +
88A TYR* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.3 48.8 + - + +
58A ILE* 5.9 0.3 - - - +
76A TYR* 6.0 1.7 - - - -
81A ALA 2.9 17.5 + - - +
82A ARG* 3.1 5.2 + - - +
84A GLU* 1.3 73.9 - - - +
86A ILE* 1.3 61.9 + - - +
88A TYR* 3.2 9.6 + - + +
89A GLY 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 4.4 16.4 - - + -
48A HIS* 3.9 37.0 - - + +
51A ALA* 4.3 1.1 - - + +
52A ALA* 3.9 22.0 - - + +
55A TYR* 3.9 25.4 - - + -
82A ARG* 3.1 40.6 + - + +
83A ASN* 3.6 12.8 - - - +
85A GLU* 1.3 76.0 - - - +
87A ALA* 1.3 62.7 + - - +
89A GLY 3.8 0.3 - - - -
90A SER* 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 4.9 7.0 - - - +
83A ASN 2.9 16.6 + - - +
84A GLU* 3.5 9.6 - - - +
86A ILE* 1.3 78.4 - - - +
88A TYR* 1.3 60.8 + - - +
90A SER* 2.7 23.3 + - - -
91A THR* 3.4 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 4.2 9.0 - - - -
84A GLU 3.1 11.0 + - - +
85A GLU* 3.5 12.6 - - + +
87A ALA* 1.3 79.6 - - - +
89A GLY* 1.3 68.0 + - - +
91A THR* 2.6 33.9 + - - -
92A LEU* 3.7 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 3.9 13.2 - - - -
55A TYR* 3.5 18.6 - - - -
85A GLU 2.8 15.6 + - - -
86A ILE 3.8 1.1 - - - -
88A TYR* 1.3 75.2 - - - +
90A SER* 1.3 60.8 + - - +
91A THR 3.1 1.1 + - - -
92A LEU* 3.1 23.1 + - - +
97A LEU* 3.2 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 3.3 30.3 + - - -
48A HIS* 3.4 49.1 + - - -
51A ALA* 4.0 0.6 - - - +
86A ILE 2.9 14.8 + - - -
87A ALA* 2.7 20.4 + - - -
89A GLY* 1.3 75.4 - - - +
91A THR* 1.3 61.8 + - - +
92A LEU 3.4 2.5 + - - +
----------------------------------------------------------
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