Contacts of the strand formed by residues 81 - 87 (chain D) in PDB entry 4XZG
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 GLU 81 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL 4.1 5.0 - - - +
77D VAL* 3.7 19.6 - - + +
78D ASN* 3.1 50.4 + - + +
79D ASN 3.2 1.3 - - - +
80D ASN* 1.3 78.1 - - - +
82D MET* 1.3 74.9 + - - +
83D VAL* 4.6 0.3 - - - +
102D ASN* 4.4 3.8 - - - +
103D VAL* 4.0 27.2 - - + +
133D VAL* 3.6 4.7 - - - -
134D VAL* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D GLU* 1.3 89.0 - - - +
83D VAL* 1.3 76.4 + - - +
84D ALA* 5.7 1.6 - - + -
103D VAL* 3.7 25.5 + - + +
131D GLU* 3.9 35.0 - - + +
132D GLY 3.5 21.3 - - - +
133D VAL* 4.4 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 5.9 0.2 - - + -
77D VAL* 3.8 24.5 - - + -
81D GLU 3.7 0.2 + - - -
82D MET* 1.3 90.4 - - - +
84D ALA* 1.3 61.0 + - - +
85D LEU* 4.9 1.8 - - + -
100D VAL* 3.7 22.4 - - + -
101D ASN 3.3 14.8 - - - +
102D ASN* 4.6 4.0 - - - +
103D VAL* 4.9 0.4 - - - +
108D VAL* 5.2 0.2 - - + -
132D GLY* 3.0 27.0 + - - +
134D VAL* 3.7 22.4 - - + -
144D MET* 5.9 0.2 - - - -
146D LEU* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D MET* 5.7 1.8 - - + -
83D VAL* 1.3 75.8 - - - +
85D LEU* 1.3 69.0 + - - +
86D GLN* 6.1 0.2 - - + -
99D LYS 3.5 0.3 - - - +
100D VAL* 3.3 4.9 - - - -
101D ASN* 2.8 47.3 + - + +
102D ASN 4.9 4.5 - - - +
103D VAL* 6.2 1.1 - - - -
132D GLY 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D VAL* 4.9 1.3 - - + -
84D ALA* 1.3 83.8 - - - +
86D GLN* 1.3 62.0 + - - +
98D ILE* 3.9 14.1 - - + -
99D LYS 3.3 2.9 - - - -
100D VAL* 4.5 14.4 - - + -
111D LEU* 4.3 7.6 - - + -
119D LEU* 4.3 19.1 - - + -
123D MET* 4.0 19.6 - - + +
130D ILE* 3.5 43.5 + - + +
132D GLY* 4.9 12.3 - - - +
146D LEU* 4.3 21.5 - - + -
148D MET* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ALA* 6.1 0.4 - - + -
85D LEU* 1.3 77.4 - - - +
87D ARG* 1.3 73.8 + - - +
98D ILE* 3.8 2.6 - - - +
99D LYS* 2.6 70.0 + - + +
101D ASN* 3.0 29.6 + - - +
123D MET* 4.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLN* 1.3 89.0 + - - +
88D ASP* 1.3 70.6 + - - +
89D PRO* 3.6 24.6 - - + +
95D LYS* 2.7 34.6 + - - +
96D ASN* 3.3 6.3 + - - +
97D ALA 2.7 30.6 + - - +
98D ILE* 3.6 20.6 - - - -
99D LYS* 4.6 2.1 - - - -
120D ALA* 3.6 23.6 - - - +
123D MET* 3.9 24.7 - - + +
124D ASP* 2.9 40.1 + - - +
----------------------------------------------------------
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