Contacts of the strand formed by residues 94 - 102 (chain D) in PDB entry 3Q3G
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 ALA 94 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LYS* 3.9 21.5 - - + -
41D GLN 3.5 21.3 - - - +
42D ARG* 4.1 6.7 - - - -
43D PRO* 4.5 6.7 - - - -
92D ASP 3.2 4.3 + - - +
93D THR* 1.3 76.3 - - - +
95D VAL* 1.3 64.4 + - - +
96D TYR* 3.6 16.5 - - + +
119D THR* 3.8 1.7 - - - -
120D VAL 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL 3.9 0.3 - - - +
40D LYS* 3.7 1.4 - - - -
41D GLN* 2.8 41.8 + - + +
94D ALA* 1.3 74.4 - - - +
96D TYR* 1.3 60.7 + - - +
97D TYR* 3.6 40.2 + - + +
117D GLY* 4.0 12.8 - - - -
118D THR 3.4 6.7 - - - +
119D THR* 4.0 23.8 - - + +
800D NA 4.2 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLN* 2.8 25.7 + - - -
22D LEU* 3.7 20.9 - - + -
38D TRP* 4.5 3.8 - - + -
39D VAL 3.5 2.7 - - - +
40D LYS* 3.7 29.6 + - + +
50D ILE* 3.6 32.8 - - + -
66D PHE* 5.6 0.4 - + - -
83D LEU* 3.8 10.1 - - + -
85D LEU* 3.6 25.5 - - + +
92D ASP* 2.6 45.8 + - - +
94D ALA* 3.6 20.0 - - + -
95D VAL* 1.3 72.5 - - - +
97D TYR* 1.3 56.5 + - - +
117D GLY* 3.4 1.1 - - - -
118D THR 2.9 19.3 + - - +
120D VAL* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLN* 3.3 19.2 + - - -
47C GLY 5.5 0.5 + - - -
48C GLN 3.7 8.5 + - - -
49C SER* 3.4 22.7 - - - -
50C PRO* 4.0 9.2 - - + -
8D GLN* 3.6 2.0 - - - -
38D TRP* 3.4 9.8 - - - -
39D VAL* 2.8 41.6 + - + +
41D GLN* 3.3 33.5 + - + -
47D LEU* 4.5 4.0 - - + -
95D VAL* 3.6 21.9 - - + +
96D TYR* 1.3 74.8 - - - +
98D CYS* 1.3 60.8 + - - +
114D TRP* 3.8 26.5 - + + -
115D GLY 3.5 17.9 - - - -
116D GLN 3.7 4.6 + - - -
117D GLY* 3.6 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 4.0 11.7 - - - -
8D GLN* 3.2 24.3 + - - -
24D CYS* 2.0 55.0 - - + -
36D MET* 4.6 4.5 - - + -
37D GLN 3.2 10.3 - - - +
38D TRP* 3.9 14.8 - - + -
97D TYR* 1.3 76.9 - - - +
99D ALA* 1.3 60.5 + - - +
114D TRP* 3.5 1.6 - - - -
115D GLY 2.8 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.9 4.0 - - - -
36D MET* 3.6 4.6 - - - +
37D GLN* 2.6 38.4 + - + +
39D VAL* 5.0 1.6 - - + -
98D CYS* 1.3 76.5 - - - +
100D SER* 1.3 58.8 + - - +
111D MET* 3.8 31.4 - - + -
113D TYR 3.1 13.5 - - - +
114D TRP* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.8 3.3 - - - +
29D PHE* 3.7 11.1 - - - -
34D ILE* 4.1 28.5 - - - +
35D TYR 3.4 7.9 - - - -
36D MET* 4.2 6.3 - - - -
37D GLN* 4.7 0.4 - - - -
99D ALA* 1.3 74.2 - - - +
101D GLU* 1.4 58.3 + - - +
111D MET* 3.5 4.4 - - - -
112D ASP* 3.2 27.4 + - - +
113D TYR* 2.9 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C TYR* 5.0 0.2 - - - +
100C TYR* 4.5 0.9 + - - -
102C LEU* 4.3 9.9 - - - +
34D ILE* 3.7 2.5 - - - -
35D TYR* 2.9 47.8 + - + +
37D GLN* 3.5 28.0 + - + +
99D ALA 4.3 0.2 - - - -
100D SER* 1.4 70.4 - - - +
102D GLY* 1.3 62.6 + - - +
103D HIS* 4.3 2.9 + - - -
108D GLY* 3.7 3.3 - - - -
109D TYR* 3.2 36.4 + - + +
110D ALA 3.4 14.5 - - - +
111D MET* 4.4 2.6 - - + +
208G ARG* 2.8 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 4.0 15.5 - - - -
100D SER* 3.8 1.0 + - - -
101D GLU* 1.3 78.1 - - - +
103D HIS* 1.3 65.8 - - - -
104D TYR* 3.5 25.2 - - - -
108D GLY 4.9 0.9 - - - +
109D TYR* 3.3 22.3 + - - +
110D ALA 4.2 1.6 + - - -
112D ASP* 3.3 14.0 + - - -
----------------------------------------------------------
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