Contacts of the strand formed by residues 97 - 102 (chain E) in PDB entry 6XAV
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 97 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E GLY 4.1 0.2 - - - +
52E ASP* 3.3 18.6 - - - -
53E GLY 3.0 12.3 + - - +
55E LEU* 4.6 3.4 - - + -
65E LEU* 3.7 29.4 - - + +
91E LEU* 3.7 40.6 - - + -
95E ASP 3.6 13.7 - - - +
96E THR* 1.3 79.3 - - - +
98E SER* 1.3 62.1 + - - +
99E GLY 4.1 0.9 + - - -
113E LEU* 3.7 29.6 - - + -
116E VAL* 3.7 19.1 - - + -
118E GLU 3.7 0.7 - - - -
119E VAL* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E GLY 3.4 7.2 - - - -
52E ASP* 3.3 22.5 - - - +
96E THR* 4.0 12.3 - - - +
97E ILE* 1.3 72.8 - - - +
99E GLY* 1.3 57.8 + - - +
117E ASN* 3.0 4.7 + - - +
118E GLU* 2.6 65.4 + - - +
121E PHE* 5.8 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PHE* 4.1 4.3 - - - -
51E GLY 3.0 29.0 + - - +
97E ILE* 4.0 4.4 + - - +
98E SER* 1.3 74.8 - - - +
100E LYS* 1.3 65.7 + - - -
101E ILE* 3.8 3.6 - - - +
113E LEU* 4.4 4.1 - - - +
115E LYS 3.3 10.8 - - - -
116E VAL* 3.9 2.9 - - - +
117E ASN* 3.4 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ASP* 3.1 43.4 + - + +
49E ILE 3.3 17.0 - - - +
50E PHE* 3.7 21.5 - - + -
99E GLY* 1.3 71.0 - - - -
101E ILE* 1.3 63.5 + - - +
113E LEU* 3.3 5.5 - - - +
114E LEU* 3.1 48.9 + - + +
115E LYS* 2.7 32.6 + - + +
117E ASN* 3.5 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LEU* 3.9 22.4 - - + -
39E LEU* 5.7 0.4 - - + -
49E ILE* 2.7 52.2 + - + +
50E PHE 3.8 9.2 - - - +
51E GLY* 3.7 20.6 - - - +
65E LEU* 5.3 0.7 - - + -
79E ILE* 3.8 34.8 - - + -
99E GLY 3.8 9.6 - - - +
100E LYS* 1.3 83.7 - - - +
102E ARG* 1.3 65.2 + - - +
111E PHE* 4.6 12.8 - - + -
112E ALA 3.3 10.8 - - - +
113E LEU* 4.1 8.5 - - + -
114E LEU* 4.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ILE* 5.1 0.9 - - - -
101E ILE* 1.3 77.2 - - - +
103E PRO* 1.3 74.6 + - + +
105E LYS* 3.5 40.6 - - - +
108E GLU* 3.5 30.7 + - - -
111E PHE* 3.4 9.9 - - - +
112E ALA* 2.9 57.0 + - + +
113E LEU 5.5 0.6 - - - -
114E LEU* 4.9 26.2 - - + +
82G TYR* 5.7 7.7 - - - +
----------------------------------------------------------
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