Contacts of the helix formed by residues 84 - 97 (chain A) in PDB entry 5I74
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 LYS 84 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 4.0 11.2 - - - +
83A GLY* 1.3 79.5 - - - +
85A LYS* 1.3 70.3 + - + +
86A VAL* 3.6 24.7 - - + +
87A ASP* 3.1 38.2 + - - +
88A PHE* 3.6 4.2 + - - +
279A LYS* 5.3 1.3 - - - +
282A TRP* 5.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 5.7 0.4 - - - -
84A LYS* 1.3 77.2 - - + +
86A VAL* 1.3 63.6 + - + +
88A PHE* 3.6 2.2 + - - +
89A LEU* 2.9 44.5 + - + +
351A ASN* 5.2 10.3 - - - +
352A LYS* 6.5 0.4 - - + -
355A ASN* 2.6 34.6 + - - +
356A ASN* 3.8 3.2 + - - +
360A ASP* 2.6 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS* 3.2 20.3 - - + -
85A LYS* 1.3 81.2 - - + +
87A ASP* 1.3 59.3 + - - +
88A PHE 3.5 0.2 - - - -
89A LEU* 3.9 12.6 - - + -
90A LEU* 2.9 53.7 + - + +
282A TRP* 4.6 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY* 4.7 3.8 - - - +
84A LYS* 3.1 34.0 + - - +
86A VAL* 1.3 80.0 - - - +
88A PHE* 1.3 63.4 + - + +
90A LEU* 3.5 3.4 + - - +
91A SER* 2.9 25.1 + - - -
278A GLY* 3.9 19.6 - - - +
279A LYS* 2.8 39.4 + - - +
281A VAL* 4.1 4.7 - - - +
282A TRP* 3.2 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 3.5 25.4 - - + -
84A LYS 3.6 1.4 + - - +
85A LYS* 3.6 4.7 + - - +
87A ASP* 1.3 79.2 - - + +
89A LEU* 1.3 65.5 + - - +
90A LEU 3.2 0.4 - - - -
91A SER* 3.5 17.7 - - - -
92A VAL* 2.9 28.2 + - - +
274A VAL* 3.4 47.6 - - + -
277A SER* 4.4 8.1 - - - -
278A GLY* 4.7 4.3 - - - -
347A PHE* 3.6 28.1 - + + +
350A TYR* 3.1 42.4 - + + -
351A ASN* 4.8 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS* 2.9 34.3 + - + +
86A VAL* 3.8 15.9 - - + +
88A PHE* 1.3 77.0 - - - +
90A LEU* 1.3 66.0 + - + +
92A VAL* 3.4 10.8 - - + +
93A ILE* 3.2 28.1 - - + +
360A ASP* 4.5 25.8 - - + +
363A VAL* 5.0 13.9 - - + -
364A THR* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 2.9 42.5 + - + +
87A ASP* 3.9 1.1 - - - +
89A LEU* 1.3 85.9 - - + +
91A SER* 1.3 59.6 + - - +
92A VAL 3.5 0.2 - - - -
93A ILE* 3.8 14.0 - - + +
94A GLY* 2.9 23.0 + - - -
281A VAL* 3.3 18.6 - - + +
282A TRP* 4.9 22.9 - - + -
285A ALA* 4.0 12.3 - - + +
286A THR* 4.2 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP 2.9 17.4 + - - -
88A PHE* 3.0 22.6 + - - -
90A LEU* 1.3 75.6 - - - +
92A VAL* 1.3 60.5 + - - +
94A GLY 3.4 1.2 + - - -
95A TYR* 2.9 23.0 + - - +
277A SER 3.8 7.4 + - - -
278A GLY* 5.0 0.2 - - - -
281A VAL* 3.6 25.6 - - - +
347A PHE* 3.1 34.0 - - - -
437A ASP 5.5 0.5 - - - +
441A ALA* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE 2.9 18.2 + - - +
89A LEU* 3.4 12.6 - - + +
91A SER* 1.3 75.3 - - - +
93A ILE* 1.3 60.1 - - - +
95A TYR* 3.3 3.9 + - - +
96A ALA* 2.9 26.7 + - + +
133A PHE* 3.6 21.1 - - + -
137A LEU* 5.2 10.5 - - + -
344A LEU* 3.6 29.6 - - + -
347A PHE* 3.9 19.6 - - + -
360A ASP* 6.5 0.4 - - + -
364A THR* 3.6 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.2 26.9 + - + +
90A LEU* 3.6 15.2 + - + +
91A SER 3.2 0.4 - - - -
92A VAL* 1.3 75.9 - - - +
94A GLY* 1.3 60.5 + - - +
96A ALA* 3.0 5.6 + - - +
97A VAL* 2.8 42.9 + - + +
285A ALA* 5.6 4.3 - - + -
289A TYR* 4.2 7.6 - - + +
363A VAL* 5.2 2.9 - - + -
364A THR* 3.6 34.8 - - + +
367A VAL* 3.9 36.8 - - + -
368A ASN* 5.5 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 2.9 17.5 + - - -
91A SER* 3.8 1.6 - - - -
93A ILE* 1.3 77.3 - - - +
95A TYR* 1.3 56.7 + - - +
97A VAL* 3.0 17.6 - - - +
281A VAL* 5.4 0.7 - - - -
285A ALA* 4.3 9.8 - - - +
437A ASP* 3.0 45.9 - - - +
438A SER* 3.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A SER 2.9 12.4 + - - +
92A VAL* 3.3 12.3 - - - +
93A ILE 3.1 0.2 - - - -
94A GLY* 1.3 78.8 - - - +
96A ALA* 1.3 64.4 + - + +
337A LEU 3.8 9.9 - - - -
338A GLY* 2.7 28.0 + - - -
341A PHE* 4.4 1.6 - - - +
343A VAL* 3.5 24.8 - - + +
344A LEU* 3.6 32.8 - - + -
347A PHE* 4.3 0.9 - - + -
437A ASP* 4.4 1.5 - - - +
438A SER* 2.7 30.9 + - - +
441A ALA* 3.4 31.9 - - + -
442A GLY 4.7 0.2 - - - -
700A 69D 3.3 59.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 2.9 16.5 + - + +
93A ILE* 3.0 6.7 + - - +
95A TYR* 1.3 85.2 - - + +
97A VAL* 1.3 56.6 + - - +
101A ASN* 3.1 9.9 - - - +
133A PHE* 5.1 8.7 - - + -
336A SER 3.4 9.0 - - - +
337A LEU* 4.5 9.2 - - + +
364A THR* 5.6 3.1 - - - +
368A ASN* 2.8 33.0 - - + +
700A 69D 3.2 17.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 2.8 28.3 + - + +
94A GLY* 3.0 11.8 - - - +
96A ALA* 1.3 76.8 - - - +
98A ASP* 1.3 64.8 + - - +
101A ASN* 3.9 7.2 - - + -
102A VAL* 5.8 0.2 - - + -
288A PRO* 5.5 2.7 - - + -
289A TYR* 3.7 26.9 - - + +
368A ASN* 3.9 20.0 - - + +
371A THR* 4.1 19.3 - - + +
434A LEU* 3.2 29.3 - - + +
437A ASP* 3.8 2.2 - - - +
438A SER* 3.0 14.4 + - - -
----------------------------------------------------------
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