Contacts of the strand formed by residues 88 - 94 (chain K) in PDB entry 3QUM
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 88 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K LYS* 4.4 6.7 - - + -
39K GLN 3.3 4.5 - - - +
40K ARG* 3.1 39.0 - - + +
41K PRO* 4.3 7.2 - - - -
86K ASP 3.0 7.1 + - - +
87K SER* 1.3 76.4 - - - +
89K VAL* 1.3 67.4 + - - +
90K TYR* 3.6 12.8 - - + -
108K SER* 4.3 3.6 - - - -
109K VAL 3.3 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K LYS* 3.5 2.1 - - - -
39K GLN* 2.8 42.9 + - + +
41K PRO* 6.4 0.9 - - + -
88K ALA* 1.3 80.3 - - - +
90K TYR* 1.3 64.6 + - - +
91K PHE* 3.9 26.4 + - + -
105K GLN 5.3 0.7 - - - +
106K GLY* 4.4 4.9 - - - -
107K THR 3.9 22.9 - - - +
108K SER* 3.9 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K GLN* 2.9 19.1 - - - +
20K ILE* 5.3 11.2 - - + +
36K TRP* 5.1 4.4 - - + -
37K VAL 3.2 9.0 - - - +
38K LYS* 3.7 34.1 + - + -
48K ILE* 3.9 23.6 - - + -
63K PHE* 5.5 1.6 - + - -
80K MET* 3.9 19.5 - - + -
82K LEU* 3.5 31.2 - - + +
86K ASP* 2.8 32.3 + - - +
88K ALA 3.6 18.8 - - - -
89K VAL* 1.3 74.6 - - - +
91K PHE* 1.3 63.5 + - - +
107K THR* 3.2 24.6 + - - +
109K VAL* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K GLN* 3.6 3.6 - - - +
36K TRP* 3.3 7.2 - - - -
37K VAL* 2.8 55.5 + - + +
39K GLN* 3.1 35.2 - - + -
45K LEU* 5.1 1.3 - - + -
89K VAL* 3.9 21.3 - - + -
90K TYR* 1.3 75.3 - - - +
92K CYS* 1.3 63.1 + - - +
103K TRP* 3.8 23.1 - + + -
104K GLY 3.7 17.3 - - - -
105K GLN 3.8 16.6 - - - -
106K GLY* 4.0 4.7 - - - -
38M GLN* 4.2 3.4 - - - -
42M GLN 4.4 4.3 - - - -
43M SER* 3.8 23.6 - - - -
44M PRO* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 92 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K LEU* 4.3 8.5 - - - -
6K GLN* 2.6 37.6 - - - +
22K CYS* 2.1 44.6 - - - -
34K MET* 3.5 15.5 - - + -
35K ASN 3.2 7.6 - - - +
36K TRP* 3.7 20.7 - - + -
91K PHE* 1.3 78.5 - - - +
93K ALA* 1.3 65.6 + - - +
103K TRP* 3.7 1.6 - - - -
104K GLY 3.5 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K LEU* 4.4 1.3 - - - -
34K MET* 3.4 7.3 - - - -
35K ASN* 2.6 44.9 + - - +
37K VAL* 5.5 2.7 - - + -
91K PHE 5.0 0.9 - - - +
92K CYS* 1.3 80.2 - - - +
94K ARG* 1.3 58.6 + - - +
100K PHE* 4.5 14.4 - - + +
102K TYR 3.1 13.5 - - - +
103K TRP* 3.9 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K VAL* 4.6 6.6 - - - +
4K LEU* 4.5 4.7 - - + +
27K TYR* 3.4 53.1 - - - +
32K SER* 3.3 22.8 + - - -
33K TRP 3.5 12.3 - - - +
34K MET* 4.3 7.2 - - + -
35K ASN* 4.3 0.2 - - - -
93K ALA* 1.3 73.4 - - - +
95K ASP* 1.3 72.0 + - - +
96K GLY* 5.0 1.3 - - - -
100K PHE 4.2 3.1 - - - -
101K ASP* 2.4 66.2 + - - +
102K TYR* 2.9 39.0 + - + +
----------------------------------------------------------
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