Contacts of the strand formed by residues 85 - 92 (chain N) in PDB entry 5M5X
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 HIS 85 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N THR* 4.2 13.7 + - - +
80N MET 3.5 12.4 + - - -
81N THR* 3.4 37.9 - - - -
82N ILE 3.0 18.5 + - - +
83N ASP 4.6 1.6 - - - +
84N LYS* 1.3 85.4 - - - +
86N ASP* 1.3 60.8 + - - +
87N TYR* 4.2 3.7 - - - -
144N LYS* 5.8 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B TRP* 4.2 11.4 - - - -
84N LYS* 3.1 28.3 - - - +
85N HIS* 1.3 75.6 - - - +
87N TYR* 1.3 74.9 + - - +
141N GLU* 3.1 43.5 - - - +
142N THR 3.9 9.6 - - - +
143N ALA* 3.9 26.4 - - + +
144N LYS 5.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59N PRO* 5.0 5.2 - - + -
61N ASN 4.3 2.1 + - - -
62N VAL* 3.2 37.2 - - + +
79N THR* 4.4 14.2 + - - -
80N MET* 3.7 43.3 + - + +
82N ILE* 3.5 34.0 - - + +
84N LYS* 3.4 22.7 + - + +
85N HIS* 4.2 0.8 - - - -
86N ASP* 1.3 105.9 - - - +
88N LYS* 1.3 67.4 + - - +
89N ILE* 5.2 1.6 - - + -
139N VAL* 3.5 27.1 - - + -
140N SER 3.4 6.5 - - - -
141N GLU* 5.4 4.3 - - + -
142N THR* 3.5 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N SER* 3.1 48.1 + - - +
77N SER* 3.8 2.8 - - - +
78N THR* 3.3 35.0 - - - +
79N THR* 5.4 0.9 - - - +
87N TYR* 1.3 78.2 - - - +
89N ILE* 1.3 69.7 + - - +
90N MET* 3.5 15.0 + - + -
139N VAL* 4.8 1.1 - - - +
140N SER* 2.4 55.0 + - - +
142N THR* 3.2 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70N LEU* 4.3 25.8 - - + -
71N PRO 4.5 5.2 - - - +
72N VAL* 5.9 2.9 - - + -
76N SER* 2.8 24.0 + - - +
78N THR* 4.6 13.7 - - + +
79N THR 4.2 18.4 - - - +
80N MET* 4.3 18.2 - - + -
87N TYR* 5.2 0.9 - - + -
88N LYS* 1.3 83.4 + - - +
90N MET* 1.3 62.8 + - - +
137N PHE* 3.6 43.5 - - + -
138N SER 3.9 4.3 - - - +
139N VAL* 4.3 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 90 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B SER* 6.0 6.5 - - - -
600B GLN* 4.2 33.7 - - + +
603B ILE* 5.8 6.7 - - + -
76N SER* 3.3 9.6 - - - -
88N LYS* 4.1 15.0 - - + -
89N ILE* 1.3 77.0 - - - +
91N ASP* 1.3 63.0 + - - +
137N PHE* 3.1 31.9 - - - -
138N SER* 2.9 28.7 + - - +
140N SER* 3.3 30.3 - - - +
142N THR* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73N ASP 5.3 0.3 - - - +
74N PHE* 4.5 2.3 - - - +
75N GLU* 2.9 50.0 + - - +
76N SER* 2.9 17.2 + - - +
90N MET* 1.3 78.7 - - - +
92N ASP* 1.3 93.3 + - - +
93N THR* 5.5 0.9 - - - -
135N LYS* 4.8 2.3 - - - +
136N VAL 4.1 0.4 - - - -
137N PHE* 3.2 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91N ASP* 1.3 91.6 + - - +
93N THR* 1.3 78.9 + - - +
94N ASP 3.2 26.9 + - - +
134N ASP 3.2 16.6 - - - +
135N LYS* 4.2 1.6 - - - -
136N VAL* 3.2 35.0 + - + +
----------------------------------------------------------
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