Contacts of the strand formed by residues 65 - 70 (chain A) in PDB entry 1QMU
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 PRO 65 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 3.5 6.1 - - - +
64A GLU* 1.3 84.4 - - - +
66A GLU* 1.3 61.3 + - - +
107A SER 3.4 19.7 - - - +
108A THR* 3.5 5.2 - - - +
109A ARG 3.2 23.2 + - - -
175A VAL* 4.3 3.6 - - + -
302A VAL* 3.8 28.9 - - + +
303A HIS* 3.7 23.3 - - + +
307A TRP* 6.3 0.4 - - + -
342A TRP* 3.5 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 3.1 28.6 + - - +
64A GLU 4.1 1.8 - - - +
65A PRO* 1.3 75.4 - - - +
67A PHE* 1.3 58.0 + - - +
109A ARG* 2.9 40.5 + - + -
111A HIS* 2.8 28.6 + - - -
172A TYR* 3.8 6.4 - - - +
173A PRO* 3.6 40.4 + - + +
174A PHE* 3.3 9.5 - - + +
175A VAL* 2.7 40.5 + - - +
176A LEU 3.8 0.3 + - - -
302A VAL* 4.8 0.2 - - - -
342A TRP* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO 3.9 0.4 + - - -
66A GLU* 1.3 73.9 - - - +
68A LYS* 1.3 87.2 + - - +
69A TYR* 3.4 31.4 - + - -
108A THR* 4.0 19.5 - - + -
109A ARG 3.1 8.8 + - - +
110A ILE* 4.2 15.7 - - + -
111A HIS* 2.8 29.1 + - - -
174A PHE* 3.8 2.2 - - - -
176A LEU* 3.5 32.8 - - + -
298A PHE* 3.7 33.0 - + - -
299A ILE* 3.7 34.8 - - + -
302A VAL* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 1.3 86.6 - - - +
69A TYR* 1.3 59.0 + - - +
70A ILE* 3.9 15.7 - - + -
111A HIS* 3.1 10.8 - - + +
168A TRP* 4.3 9.4 - - + -
169A LEU* 3.0 31.6 - - + -
174A PHE* 3.3 43.7 - - + -
176A LEU 3.2 3.4 + - - -
177A SER* 2.7 63.7 + - - +
178A ALA 3.2 2.8 + - - -
260A ASN* 2.8 24.1 + - - -
266A CYS* 3.6 3.8 - - - -
268A GLU* 3.0 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.4 27.8 - + - -
68A LYS* 1.3 72.2 - - - +
70A ILE* 1.3 65.2 + - - +
84A LEU* 3.5 22.4 - - + +
87A LEU* 3.9 25.1 - - + -
110A ILE* 5.5 0.2 - - + -
111A HIS 3.0 8.5 + - - +
112A ILE* 3.7 7.9 - - + -
113A MET 3.0 26.0 + - - -
168A TRP* 4.7 0.5 - - - -
178A ALA* 3.4 34.1 - - + -
180A LEU* 4.6 9.4 - - + -
217A TYR* 4.3 0.3 - - - -
271A ILE* 5.0 2.0 - - + -
295A LEU* 2.7 47.4 + - + +
298A PHE* 3.5 18.2 - + - +
299A ILE* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 3.9 22.0 - - + +
69A TYR* 1.3 81.9 - - - +
71A GLY* 1.3 57.0 + - - +
73A MET* 5.8 2.0 - - + -
84A LEU* 3.9 3.1 - - - -
113A MET* 3.4 23.3 - - + -
116A MET* 4.0 17.9 - - + -
165A VAL* 4.8 3.4 - - + -
168A TRP* 3.4 33.2 - - + -
177A SER* 5.0 0.2 - - - +
178A ALA 3.0 7.9 + - - +
179A ASN* 3.0 11.0 - - + +
180A LEU* 2.6 35.9 + - - +
256A MET* 3.9 31.4 - - + -
268A GLU* 4.2 5.2 - - - +
----------------------------------------------------------
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