Contacts of the strand formed by residues 64 - 68 (chain A) in PDB entry 2QMQ
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 64 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG 3.9 0.6 + - - -
63A PRO* 1.3 72.7 - - - +
65A ILE* 1.3 62.7 + - - +
66A PHE* 3.5 1.3 + - + -
96A VAL* 3.5 28.5 - - + +
98A VAL* 4.5 9.6 - - + -
137A PHE* 3.9 21.3 - - + -
139A THR 3.1 13.3 + - - +
140A ILE* 3.1 12.1 - - + +
141A ILE* 2.8 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO 3.8 0.6 + - - -
64A ALA* 1.3 71.4 - - - +
66A PHE* 1.3 59.4 + - - +
67A THR* 4.2 4.8 + - + +
83A PHE* 3.8 30.1 - - + -
92A ILE* 3.8 27.8 - - + -
95A PHE* 3.6 39.9 - - + -
96A VAL 2.9 12.4 + - - +
97A ARG* 3.3 8.6 - - + +
98A VAL* 2.8 27.7 + - - +
141A ILE* 3.5 15.9 - - + -
143A VAL* 4.1 17.3 - - + -
307A PHE* 5.8 3.4 - - + -
311A LEU* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 4.8 0.4 - - + -
65A ILE* 1.3 73.8 - - - +
67A THR* 1.3 63.3 + - - +
68A TYR* 4.8 0.7 - + - -
98A VAL* 3.3 34.3 - - + -
100A VAL* 3.5 27.4 - - + -
128A ILE* 3.8 27.6 - - + -
131A ILE* 3.9 15.9 - - + -
132A LEU* 3.8 29.6 - - + -
140A ILE* 3.8 29.8 - - + -
141A ILE 2.9 9.2 + - - +
142A GLY* 3.3 4.3 - - - -
143A VAL 2.9 21.7 + - - +
152A LEU* 3.8 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.2 6.3 - - + +
66A PHE* 1.3 78.1 - - - +
68A TYR* 1.3 61.1 - - - +
75A TYR* 4.6 1.2 - - - +
79A PHE* 3.6 22.0 - - + -
83A PHE* 3.8 22.4 - - + -
98A VAL 2.9 9.2 + - - +
99A HIS* 2.8 48.3 + - + +
100A VAL* 3.1 29.5 + - - +
143A VAL* 3.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 4.8 3.1 - - + +
67A THR* 1.3 73.2 - - - +
69A HIS* 1.3 75.8 + + - +
79A PHE* 3.6 3.6 - - - -
100A VAL* 3.6 36.4 - - + +
102A ALA* 3.6 31.4 - - + +
103A PRO* 4.2 1.0 - - - +
124A LEU* 3.7 28.0 + - - +
127A MET* 5.6 0.5 - - - -
128A ILE* 4.3 15.9 - - + -
131A ILE* 5.9 0.2 - - + -
143A VAL 3.0 7.1 + - - -
144A GLY* 3.3 4.0 - - - -
145A VAL 3.3 22.7 + - - -
148A GLY* 3.4 18.2 - - - +
151A ILE* 3.4 46.7 - - + -
152A LEU* 3.9 10.8 - - + -
233A TYR* 3.7 7.9 - - - -
----------------------------------------------------------
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