Contacts of the helix formed by residues 97 - 110 (chain D) in PDB entry 1EQB
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 SER 97 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C HIS* 4.0 16.0 + - - -
262C GLY 5.2 0.3 + - - -
263C GLY 5.4 0.4 - - - -
265C LEU* 6.2 1.1 - - - -
95D PRO* 3.2 2.1 - - - +
96D HIS* 1.3 79.4 - - - +
98D GLY* 1.3 61.3 + - - +
99D SER* 3.5 3.3 + - - -
100D GLN* 2.6 34.7 + - - +
101D ALA* 3.0 21.5 + - - +
236D GLY* 3.7 4.5 - - - -
237D GLY* 3.2 22.0 - - - +
4291D PLP 3.5 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D SER* 1.3 73.4 - - - +
99D SER* 1.3 65.9 + - - +
101D ALA* 3.3 5.7 + - - +
102D ASN* 3.0 28.6 + - - +
224D THR* 6.5 0.2 - - - -
225D THR 5.1 2.0 - - - -
226D THR* 3.5 19.7 - - - +
237D GLY* 4.5 1.3 - - - -
4291D PLP 3.4 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C GLY 4.1 7.9 - - - -
261C GLN* 3.5 11.5 - - - -
262C GLY* 3.2 23.0 + - - -
97D SER* 3.4 4.0 - - - -
98D GLY* 1.3 74.9 - - - +
100D GLN* 1.3 59.3 + - - +
102D ASN* 3.3 3.5 + - - +
103D PHE* 2.8 29.5 + - - +
126D HIS* 4.5 1.2 - - - -
128D THR* 3.9 27.7 - - - +
135D PHE* 4.1 4.5 - - - -
4291D PLP 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C HIS* 3.5 15.0 - - - -
100C GLN* 3.5 40.6 - - - +
103C PHE* 6.3 1.0 - - - -
260C GLY 3.2 22.8 + - - -
261C GLN* 4.1 4.2 - - - +
95D PRO* 4.4 1.6 - - + -
96D HIS* 4.0 4.9 - - + +
97D SER* 2.6 35.1 + - - +
98D GLY 3.2 0.6 - - - -
99D SER* 1.3 80.0 - - - +
101D ALA* 1.3 66.1 + - - +
103D PHE* 3.2 14.5 + - + +
104D ALA* 3.1 22.5 + - - +
135D PHE* 6.0 0.2 - - - -
256D VAL* 5.8 0.2 - - - +
261D GLN* 3.5 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D PRO* 3.8 23.5 - - + +
97D SER 3.0 18.1 + - - +
98D GLY* 3.6 6.1 - - - +
100D GLN* 1.3 75.6 - - - +
102D ASN* 1.3 63.8 + - - +
104D ALA* 3.2 13.9 + - - +
105D VAL* 3.2 16.3 + - - +
224D THR* 4.0 19.9 - - + +
225D THR 4.9 0.7 - - - +
237D GLY* 4.3 0.9 - - - -
238D LEU 4.0 17.3 - - - +
239D ILE* 4.2 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLY 3.0 16.6 + - - +
99D SER 3.6 7.4 - - - +
101D ALA* 1.3 73.7 - - - +
103D PHE* 1.3 65.0 + - - +
105D VAL* 3.1 12.1 + - - +
106D TYR* 3.0 31.0 + - + -
128D THR* 2.7 32.9 + - - +
129D HIS* 4.3 3.2 + - - -
135D PHE* 4.9 0.2 - - + -
198D PHE* 3.3 16.0 - - + -
200D ASP* 2.9 20.9 + - - +
224D THR* 2.8 28.4 + - - -
4291D PLP 3.7 5.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C GLN* 6.2 1.1 - - - -
103C PHE* 3.6 39.9 - + - -
135C PHE* 4.5 11.9 - - + -
139C LEU* 5.2 2.9 - - + -
99D SER 2.8 20.1 + - - +
100D GLN* 3.2 17.0 + - + +
102D ASN* 1.3 72.2 - - - +
104D ALA* 1.3 65.5 - - + +
106D TYR* 3.3 3.7 + - + +
107D THR* 3.0 53.5 + - + +
135D PHE* 3.5 42.5 - + + -
139D LEU* 4.6 8.3 - - + -
140D TYR* 6.0 0.2 - - - -
255D ALA 5.5 0.4 - - - -
259D GLY 5.3 0.9 - - - -
260D GLY* 4.3 26.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLN 3.1 11.7 + - - +
101D ALA 3.3 9.9 - - - +
102D ASN 3.1 0.2 - - - -
103D PHE* 1.3 80.5 - - + +
105D VAL* 1.3 64.0 + - - +
107D THR* 3.1 8.7 + - - -
108D ALA* 2.9 26.6 + - - +
239D ILE* 4.1 6.5 - - + -
252D LEU* 5.1 1.6 - - + -
255D ALA* 3.3 15.0 - - + +
256D VAL* 3.8 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ALA 3.7 4.7 - - - +
102D ASN 3.1 7.5 + - - +
104D ALA* 1.3 76.7 - - - +
106D TYR* 1.3 64.7 + - - +
108D ALA 3.4 0.2 + - - -
109D LEU* 3.2 33.1 + - + +
169D MET* 3.9 14.3 - - + +
198D PHE* 3.8 32.5 - - + -
222D VAL* 3.8 20.9 - - + -
224D THR* 3.6 31.4 - - + -
239D ILE* 4.6 4.5 - - + -
252D LEU* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ASN* 3.0 41.2 + - + -
103D PHE* 3.6 6.7 - - - +
104D ALA 3.2 0.2 - - - -
105D VAL* 1.3 77.5 - - - +
107D THR* 1.3 59.8 + - + +
108D ALA 3.2 0.3 + - - -
110D LEU* 2.8 50.1 + - + +
116D VAL* 4.6 12.1 - - + -
128D THR 2.4 30.5 + - - -
129D HIS* 3.8 1.9 - - - -
130D GLY* 5.0 0.2 - - - -
135D PHE* 3.8 18.2 - + + -
136D SER* 3.5 12.2 - - - -
140D TYR* 3.5 42.3 + + + +
142D ILE* 5.3 2.1 - - + +
169D MET* 4.9 5.2 - - - -
171D ILE* 3.1 29.9 - - + +
198D PHE* 4.5 9.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C PHE* 5.9 2.7 - - + -
138C LYS* 5.7 8.7 - - - +
139C LEU* 5.8 7.6 - - + -
103D PHE* 3.0 50.7 + - + +
104D ALA* 3.1 11.6 + - - -
106D TYR* 1.3 79.6 - - + +
108D ALA* 1.3 58.7 + - - +
110D LEU 3.9 11.7 - - - +
111D GLU* 5.5 0.5 - - - +
139D LEU* 5.8 2.0 - - + -
140D TYR* 3.9 14.8 - - - +
255D ALA* 4.0 10.5 + - - +
259D GLY 6.0 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ALA 2.9 17.8 + - - +
105D VAL 4.0 3.4 - - - +
106D TYR 3.1 0.4 - - - -
107D THR* 1.3 79.5 + - - +
109D LEU* 1.3 67.4 + - + +
110D LEU 5.1 0.2 - - - -
251D LYS* 3.7 37.5 + - + +
252D LEU* 4.0 17.9 - - + -
255D ALA* 3.4 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D VAL* 3.2 24.0 + - + +
108D ALA* 1.3 91.2 - - + +
110D LEU* 1.3 65.8 + - - +
114D ASP* 4.7 0.5 - - - +
169D MET* 3.5 29.6 - - + -
196D TYR* 4.0 47.8 + - + +
198D PHE* 5.7 0.7 - - + -
222D VAL* 4.0 18.8 - - + -
248D LEU* 3.5 29.4 - - + -
251D LYS* 5.4 3.1 - - + -
252D LEU* 5.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D TYR* 2.8 31.0 + - + +
107D THR* 3.9 12.5 - - - +
108D ALA 5.1 0.2 - - - -
109D LEU* 1.3 91.6 - - + +
111D GLU* 1.3 72.5 + - - +
112D PRO* 4.6 1.7 - - - +
114D ASP* 3.5 11.0 - - + +
116D VAL* 3.4 31.0 - - + -
140D TYR* 4.0 15.0 + - + -
168D LYS* 3.7 32.5 - - + +
169D MET* 3.9 33.0 - - + -
196D TYR* 4.9 2.5 - - + -
----------------------------------------------------------
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