Contacts of the strand formed by residues 100 - 106 (chain E) in PDB entry 6NZD
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 ILE 100 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLN* 3.9 18.6 - - - +
135A ILE* 4.1 5.8 - - + -
94E THR* 3.7 41.3 - - + +
95E MET* 3.7 20.4 - - - +
97E ASN* 3.0 35.3 + - + +
98E PRO 4.3 1.4 - - - +
99E SER* 1.3 80.0 - - - +
101E VAL* 1.3 63.2 + - - +
102E GLY 3.7 21.1 - - - +
168E VAL* 4.0 21.8 - - + -
169E HIS 3.5 5.8 - - - +
170E LYS* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E MET* 3.5 10.2 - - - +
98E PRO 4.6 6.1 - - - +
99E SER 3.6 3.6 + - - +
100E ILE* 1.3 76.5 - - - +
102E GLY* 1.3 56.9 + - - +
117E GLY* 3.3 7.4 - - - -
118E THR* 2.9 29.9 + - + +
169E HIS* 2.8 48.1 + - + +
171E MET* 4.0 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E MET* 3.7 6.1 - - - -
100E ILE* 3.7 6.6 - - - +
101E VAL* 1.3 78.8 - - - +
103E VAL* 1.3 64.0 + - - +
116E ARG 3.3 12.1 - - - -
118E THR* 3.4 14.7 + - - -
119E LEU* 4.0 5.2 - - - -
168E VAL* 3.6 1.6 - - - -
169E HIS* 2.8 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 4.5 3.6 - - + -
91E LEU* 3.9 43.1 - - + +
94E THR* 4.5 17.0 - - + -
95E MET* 4.0 5.6 - - + -
102E GLY* 1.3 75.3 - - - +
104E LEU* 1.3 66.8 + - - +
115E CYS* 3.1 3.4 - - - +
116E ARG* 2.9 51.5 + - + +
119E LEU* 3.9 4.0 - - - +
166E VAL* 4.2 14.4 - - + -
167E ALA 3.2 13.9 - - - +
168E VAL* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LEU* 5.3 0.4 - - - -
103E VAL* 1.3 78.9 - - - +
105E CYS* 1.3 75.0 + - - +
106E THR* 3.9 18.6 - - + +
112E ASN* 3.7 14.4 - - - +
114E GLY 3.5 5.2 - - - -
115E CYS* 3.8 13.5 - - + -
119E LEU* 3.9 14.3 - - + +
120E SER 3.1 33.2 - - - +
123E HIS* 4.4 5.4 - - + -
124E ALA* 4.1 14.6 - - + +
127E ILE* 3.8 20.2 - - + -
166E VAL* 3.2 8.0 - - - +
167E ALA 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA* 4.4 4.5 - - + -
87E LEU* 4.5 17.3 - - + -
91E LEU* 4.8 6.3 - - + -
104E LEU* 1.3 75.4 - - - +
106E THR* 1.3 55.5 + - - +
112E ASN* 3.2 7.8 - - - +
113E LEU* 2.7 46.1 + - + -
114E GLY 2.9 13.4 + - - +
164E ILE* 3.1 45.8 - - - -
165E THR 3.4 4.7 - - - -
166E VAL* 4.3 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E LEU* 3.9 9.2 - - + -
105E CYS* 1.3 74.6 - - - +
107E ASP* 1.3 69.0 + - - +
110E GLY* 3.4 6.6 - - - -
111E LEU 3.2 22.4 + - - -
113E LEU* 3.8 6.7 - - - +
124E ALA* 3.4 21.8 - - - +
127E ILE* 4.2 3.1 - - + -
128E SER* 3.8 26.0 - - - +
164E ILE* 3.6 5.2 - - - +
165E THR* 2.9 49.2 + - - +
----------------------------------------------------------
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