Contacts of the strand formed by residues 94 - 100 (chain D) in PDB entry 3QEL
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 ILE 94 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLY* 3.6 6.7 - - - +
37D ILE 5.5 0.4 - - - -
38D ALA* 3.9 27.4 - - + +
88D LEU* 3.3 32.3 - - + +
89D MET* 3.9 23.5 + - + +
92D ARG* 3.4 20.8 + - + +
93D LYS* 1.3 72.8 - - - +
95D GLN* 1.3 60.6 + - - +
96D GLY 3.0 32.0 + - - +
97D VAL* 4.2 8.1 - - + -
121D THR* 4.1 12.0 + - + +
317D PRO* 3.2 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ILE* 4.2 30.3 - - + -
36D GLY 2.9 13.9 + - - +
93D LYS 3.7 2.6 + - - -
94D ILE* 1.3 73.7 - - - +
96D GLY* 1.3 57.2 + - - +
121D THR* 4.5 0.2 - - - -
122D PRO* 3.2 27.3 - - - +
300D ILE* 4.4 7.5 - - + +
304D ALA* 5.8 2.9 - - + -
314D ILE* 5.5 5.8 - - + -
315D PRO 5.7 2.0 - - - +
317D PRO* 4.1 12.3 - - + +
335D LEU* 4.8 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D GLY 3.7 3.2 + - - -
37D ILE* 3.7 3.5 - - - -
38D ALA 3.2 12.6 + - - -
94D ILE* 3.0 20.6 - - - +
95D GLN* 1.3 80.9 - - - +
97D VAL* 1.3 63.2 + - - -
121D THR* 4.2 2.7 - - - -
122D PRO* 3.5 10.8 - - - -
300D ILE* 3.5 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ALA* 3.3 12.3 - - + +
40D ILE* 3.7 29.4 - - + -
85D ILE* 5.0 13.9 - - + -
89D MET* 5.8 1.6 - - - -
94D ILE* 4.2 12.3 - - + -
96D GLY* 1.3 79.7 - - - +
98D VAL* 1.3 76.1 + - - +
99D PHE* 4.4 10.3 - - + -
121D THR* 4.5 8.1 - - + -
122D PRO 3.1 6.5 + - - -
123D ILE* 3.6 27.7 - - + -
124D LEU 2.9 26.2 + - - -
300D ILE* 3.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 4.5 8.9 - - + +
38D ALA 2.7 9.3 + - - +
39D VAL* 3.2 26.0 - - + +
40D ILE* 2.7 33.8 + - - +
97D VAL* 1.3 80.1 - - - +
99D PHE* 1.3 57.4 + - - +
124D LEU* 3.9 6.7 - - + -
126D ILE* 3.5 32.1 - - + -
293D VAL* 4.5 9.6 - - + -
296D GLY* 3.5 33.9 - - - +
297D ILE* 4.3 3.8 - - + +
300D ILE* 4.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ILE* 3.7 25.4 - - + -
42D VAL* 3.8 19.7 - - + -
73D MET* 3.6 33.2 - - + -
81D ILE* 4.2 11.9 - - + -
85D ILE* 4.9 0.2 - - + -
97D VAL* 4.4 7.4 - - + -
98D VAL* 1.3 74.8 - - - +
100D ALA* 1.3 63.4 + - - +
101D ASP* 4.0 9.0 - - + -
108D ILE* 3.7 26.7 - - + -
112D LEU* 3.7 32.8 - - + -
123D ILE* 4.6 1.8 - - + -
124D LEU 2.9 16.6 + - - +
126D ILE* 3.1 28.9 + - - +
130D SER* 3.4 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ILE 3.0 6.8 + - - +
41D LEU* 3.4 20.6 - - + +
42D VAL* 2.9 25.6 + - - +
98D VAL* 4.3 0.4 - - + -
99D PHE* 1.3 77.8 - - - +
101D ASP* 1.3 60.8 + - - +
126D ILE* 4.0 7.2 - - + -
127D HIS* 3.7 14.6 - - + -
289D LEU* 3.6 31.9 - - + -
----------------------------------------------------------
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