Contacts of the helix formed by residues 88 - 103 (chain B) in PDB entry 3U44
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 THR 88 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 4.6 13.5 + - + -
87B LEU* 1.3 75.4 - - - +
89B SER* 1.3 73.2 + - - +
90B THR* 3.8 18.2 - - + +
91B GLY* 2.8 17.0 + - - -
92B VAL* 3.0 13.0 + - - +
183B SER* 4.9 0.2 - - - -
546B GLN* 2.9 25.5 + - - +
550B GLU* 2.7 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU 4.0 0.8 + - - -
88B THR* 1.3 79.0 - - - +
90B THR* 1.3 62.9 + - - +
92B VAL* 3.3 11.6 + - - +
93B GLN* 3.1 31.1 + - - +
124B GLU* 3.9 23.2 + - - +
183B SER* 4.7 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR* 3.8 11.3 - - + +
89B SER* 1.3 76.3 - - - +
91B GLY* 1.3 62.9 + - - +
93B GLN* 3.2 13.9 + - - +
94B MET* 2.9 37.8 + - - +
547B LEU* 4.6 15.7 - - + +
550B GLU* 3.6 14.0 + - - -
571B ALA 5.3 0.7 - - - +
572B GLY* 5.3 3.6 - - - -
575B SER* 3.2 35.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.6 7.9 - - - -
88B THR 2.8 9.0 + - - -
90B THR* 1.3 82.4 + - - +
92B VAL* 1.3 61.6 + - - +
94B MET* 3.5 11.7 + - - +
95B LEU 3.1 16.5 + - - -
550B GLU* 4.2 20.5 + - - -
554B MET* 3.5 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.4 22.4 - - + +
88B THR 3.0 16.1 + - - +
89B SER* 3.5 11.0 - - - +
90B THR 3.2 0.2 - - - -
91B GLY* 1.3 75.0 - - - +
93B GLN* 1.3 54.6 + - - +
95B LEU* 3.2 9.1 + - + +
96B LEU* 2.7 47.5 + - + +
124B GLU* 4.0 18.4 - - + +
127B LEU* 5.7 1.1 - - + -
172B MET* 4.0 24.2 - - + -
176B LEU* 5.5 1.8 - - + -
182B HIS* 4.3 24.2 - - + +
183B SER* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 3.1 18.4 + - - +
90B THR* 3.2 14.6 + - - +
92B VAL* 1.3 73.8 - - - +
94B MET* 1.3 60.4 + - + +
96B LEU* 3.2 4.0 + - - -
97B ARG* 2.8 34.6 + - - +
120B THR* 3.1 32.8 + - + +
121B ALA* 3.6 29.9 - - - +
124B GLU* 3.8 28.9 + - + -
125B ARG* 6.1 0.2 - - - +
571B ALA* 5.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 2.9 24.5 + - - +
91B GLY* 3.6 11.7 - - - +
92B VAL 3.3 0.2 - - - -
93B GLN* 1.3 76.9 - - - +
95B LEU* 1.3 63.6 + - - +
97B ARG* 3.4 1.9 + - - +
98B LYS 3.3 13.7 + - - -
547B LEU* 3.5 32.3 - - + +
550B GLU* 4.4 4.5 - - - -
551B PHE* 3.7 51.8 - - + -
554B MET* 4.7 5.8 - - + -
555B MET* 3.5 25.3 - - + +
568B MET* 3.8 35.9 - - + +
572B GLY* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLY 3.1 4.5 + - - +
92B VAL* 3.3 11.9 - - - +
94B MET* 1.3 79.3 - - - +
96B LEU* 1.3 64.1 + - + +
98B LYS* 2.9 24.0 + - + +
99B LEU* 3.0 42.2 + - + +
172B MET* 3.9 24.2 - - + -
175B SER* 4.2 19.3 - - - +
176B LEU* 3.8 31.2 - - + -
554B MET* 3.6 36.0 - - + +
555B MET* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 2.7 34.9 + - + +
93B GLN* 3.4 6.7 - - - +
95B LEU* 1.3 73.1 - - + +
97B ARG* 1.3 52.8 + - - +
99B LEU* 2.8 20.4 + - + +
100B ILE* 2.7 42.2 + - + +
120B THR* 3.6 14.4 - - - +
123B VAL* 4.3 11.9 - - + -
124B GLU* 3.5 44.4 - - + +
127B LEU* 3.9 22.4 - - + -
168B LEU* 4.7 10.8 - - + -
172B MET* 4.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLN* 2.8 23.3 + - - +
94B MET 3.8 4.9 - - - +
96B LEU* 1.3 72.6 - - - +
98B LYS* 1.3 56.6 + - - +
100B ILE* 3.0 31.7 - - + +
101B GLU* 3.0 34.9 - - + +
115B ASP 5.2 3.2 + - - -
116B LYS 4.5 0.8 + - - -
117B SER* 2.9 51.4 + - - +
120B THR* 3.1 25.2 + - - +
555B MET* 5.6 1.8 - - - -
564B LEU* 4.1 28.2 - - + +
568B MET* 3.4 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B MET 3.3 3.7 + - - +
95B LEU* 2.9 17.6 + - + +
97B ARG* 1.3 78.5 - - - +
99B LEU* 1.3 71.5 + - + +
101B GLU* 3.3 20.4 - - - +
102B GLU* 3.6 24.9 - - - +
554B MET 4.2 10.8 + - - +
555B MET* 3.8 24.6 - - + -
558B ASP* 3.0 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.0 40.6 + - + +
96B LEU* 2.8 15.0 + - + +
98B LYS* 1.3 83.0 - - + +
100B ILE* 1.3 65.4 + - - +
101B GLU 3.0 1.7 + - - -
102B GLU* 3.3 16.4 + - - +
103B HIS* 3.0 30.0 + - - +
168B LEU* 3.7 22.7 - - + +
171B GLN* 3.6 17.0 - - + +
172B MET* 3.5 37.5 - - + +
175B SER* 4.6 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 2.7 31.0 + - + +
97B ARG* 3.0 37.5 - - + +
99B LEU* 1.3 70.8 - - - +
101B GLU* 1.3 69.7 + - + +
104B LYS* 2.8 36.4 + - - +
107B PHE* 4.3 9.3 - - + -
114B SER* 3.0 33.7 - - - +
115B ASP* 4.8 2.9 - - - +
116B LYS 5.4 1.3 - - - +
119B PHE* 5.1 10.8 - - + -
120B THR* 5.3 9.4 - - - +
123B VAL* 5.9 1.6 - - + -
168B LEU* 3.7 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ARG* 3.0 32.9 - - + +
98B LYS* 3.3 11.7 - - - +
99B LEU 3.0 0.4 - - - -
100B ILE* 1.3 89.5 - - - +
102B GLU* 1.3 64.7 + - - +
104B LYS* 3.1 38.4 + - - +
105B GLN* 4.1 2.3 - - - +
564B LEU* 4.5 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LYS* 3.6 26.7 - - - +
99B LEU* 3.5 17.1 - - - +
101B GLU* 1.3 77.2 - - + +
103B HIS* 1.3 88.3 + - + +
104B LYS 3.1 0.2 - - - -
105B GLN* 2.7 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.0 17.9 + - + +
100B ILE 4.0 0.7 - - - -
102B GLU* 1.3 105.3 - - + +
104B LYS* 1.3 65.4 + - - +
105B GLN* 3.3 2.5 - - - -
106B GLU* 3.2 44.2 + - - +
107B PHE* 3.7 11.4 - - + -
167B ILE* 3.9 19.3 - - + -
168B LEU* 4.8 6.5 - - + -
171B GLN* 3.2 49.0 + - + +
----------------------------------------------------------
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