Contacts of the helix formed by residues 88 - 99 (chain D) in PDB entry 5MKV
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 ASP 88 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PHE* 3.8 4.8 - - - +
77D GLN* 3.3 28.5 - - + +
85D SER 5.0 2.0 - - - +
86D ALA 3.8 4.6 + - - +
87D ASP* 1.3 75.5 - - - +
89D PHE* 1.3 58.9 + - - +
90D PHE* 2.8 19.9 + - - +
91D GLN* 2.9 18.0 + - - +
92D GLY* 2.7 29.8 + - - -
130D LYS* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PHE* 3.8 24.7 - + + -
77D GLN* 3.0 33.2 - - + +
88D ASP* 1.3 76.0 - - - +
90D PHE* 1.4 51.2 + - - +
93D THR* 2.7 38.1 + - + +
104D ILE* 3.9 13.2 - - + -
106D ASP* 3.6 42.6 - - + -
123D TRP* 3.8 23.6 - + - -
126D TRP* 4.1 8.3 - + + -
127D ALA* 3.8 38.8 - - + -
130D LYS* 3.7 15.9 - - + -
131D SER* 3.6 10.3 - - - +
135D TYR* 5.0 1.1 - + - -
137D LEU* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ASP* 2.8 11.4 + - - +
89D PHE* 1.4 78.0 - - - +
91D GLN* 1.3 86.2 + - + +
93D THR* 3.3 3.9 + - - -
94D LYS* 3.0 44.2 + - + +
130D LYS* 3.4 18.8 - - + +
132D CYS* 3.4 28.7 - - - -
461D VAL* 4.0 10.5 - - + -
463D GLU* 3.6 47.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ALA 5.3 1.8 - - - +
87D ASP* 3.6 20.9 - - - +
88D ASP* 2.9 24.7 + - - +
90D PHE* 1.3 92.3 - - + +
92D GLY* 1.3 58.8 + - - +
94D LYS* 3.4 18.6 + - - +
95D ALA* 3.0 27.5 + - - +
426D ASN* 2.9 37.4 + - - +
427D SER* 4.0 4.6 - - - +
428D SER 5.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PHE* 3.5 31.6 - - - -
87D ASP* 4.3 8.7 - - - +
88D ASP 2.7 23.3 + - - +
91D GLN* 1.3 75.3 - - - +
93D THR* 1.3 55.4 + - - +
95D ALA* 3.3 8.0 + - - +
96D ALA* 2.9 26.7 + - - +
333D HIS* 5.2 0.4 - - - -
358D THR* 3.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PHE* 3.8 20.2 - - + -
89D PHE* 2.7 26.5 + - + +
90D PHE 3.3 6.1 + - - -
91D GLN 3.3 0.2 - - - -
92D GLY* 1.3 75.0 - - - +
94D LYS* 1.3 63.8 + - - +
96D ALA* 3.7 5.1 - - - +
97D LEU* 3.0 28.8 + - - +
104D ILE* 4.0 9.0 - - + -
131D SER* 3.5 16.4 - - - +
132D CYS* 2.8 27.9 + - - +
133D CYS* 3.8 18.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D PHE* 3.0 35.6 + - + +
91D GLN* 3.5 21.3 + - - +
93D THR* 1.3 78.5 + - - +
95D ALA* 1.3 57.2 + - - +
97D LEU* 3.4 2.8 + - - +
98D ALA* 3.0 27.1 + - - +
132D CYS* 4.1 11.8 - - - -
426D ASN* 4.0 12.7 - - - +
459D LEU* 3.6 35.4 - - + +
461D VAL* 4.0 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ASP* 6.1 0.9 - - - +
91D GLN 3.0 15.1 + - - +
92D GLY* 3.5 10.5 - - - +
94D LYS* 1.3 74.5 - - - +
96D ALA* 1.3 65.4 + - - +
98D ALA* 3.1 13.0 + - - +
99D GLY 3.2 9.2 + - - -
333D HIS* 5.3 0.7 - - + -
358D THR* 4.0 9.9 - - + -
359D GLU* 3.4 14.9 - - + +
426D ASN* 3.6 27.4 - - - +
606D EDO 3.7 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PHE* 5.1 0.2 - - + -
92D GLY 2.9 15.4 + - - +
93D THR* 3.7 6.7 - - - +
94D LYS 3.3 0.2 - - - -
95D ALA* 1.3 74.3 - - - +
97D LEU* 1.3 64.4 + - - +
99D GLY* 3.0 12.3 + - - -
100D GLY 3.2 0.3 + - - -
101D THR* 3.0 39.7 + - + +
104D ILE* 4.1 13.7 - - + -
133D CYS* 5.3 1.1 - - - -
358D THR* 3.5 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D THR 3.0 21.6 + - - +
94D LYS 3.8 3.6 - - - +
96D ALA* 1.3 77.3 - - - +
98D ALA* 1.3 63.1 + - - +
100D GLY* 3.0 11.4 + - - -
101D THR 3.3 20.2 - - - +
102D THR* 3.9 22.4 - - + -
132D CYS* 3.7 25.8 - - + +
133D CYS* 4.1 10.8 - - + -
446D VAL* 3.5 20.6 - - + +
448D SER* 4.1 6.1 - - - -
453D VAL* 4.0 28.0 - - + -
454D LEU* 4.9 0.2 - - - +
459D LEU* 4.7 7.1 - - + +
461D VAL* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LYS 3.0 15.2 + - - +
95D ALA 3.1 10.3 + - - +
97D LEU* 1.3 76.4 - - - +
99D GLY* 1.3 56.0 + - - +
359D GLU* 3.8 8.7 - - - +
426D ASN* 3.6 23.1 - - - +
443D PRO* 3.1 18.7 - - - +
454D LEU* 4.1 9.3 - - - +
459D LEU* 4.0 20.1 - - + +
605D EDO 4.4 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ALA 3.2 5.9 + - - -
96D ALA 3.0 8.5 + - - -
98D ALA* 1.3 77.1 - - - +
100D GLY* 1.4 57.0 + - - +
101D THR* 3.6 3.6 - - - -
358D THR 5.2 0.9 - - - -
359D GLU* 3.2 27.4 + - - +
362D MET* 3.8 21.0 + - - +
363D SER* 4.9 3.3 + - - -
412D TRP* 4.1 2.9 - - - -
443D PRO* 3.7 16.3 - - - +
----------------------------------------------------------
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