Contacts of the helix formed by residues 92 - 101 (chain A) in PDB entry 3DOW
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 THR 92 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER 2.8 16.0 + - - +
56A ASP* 3.0 15.0 + - - -
57A LEU 2.7 20.1 + - - -
58A THR* 3.8 5.6 - - - +
90A SER 3.8 0.4 + - - -
91A ALA* 1.3 77.4 - - - +
93A MET* 1.3 60.2 + - - +
94A GLY* 3.4 4.7 - - - +
95A GLN* 3.2 50.9 + - + +
96A LEU* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 4.1 7.1 - - + +
33A VAL* 5.3 3.4 - - - -
53A VAL* 3.9 25.6 - - + -
54A PRO 3.7 13.7 - - - +
57A LEU* 2.8 34.9 + - + +
58A THR 4.3 1.3 - - - +
59A VAL* 3.5 25.4 - - + -
62A PHE* 3.7 36.3 - - + -
92A THR* 1.3 71.4 + - - +
94A GLY* 1.3 60.6 + - - +
96A LEU* 3.4 31.5 - - + +
97A TYR* 2.9 29.8 + - - +
107A LEU* 4.5 3.2 - - + +
109A ILE* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 4.4 7.9 - - - -
55A SER* 3.0 32.3 + - - -
92A THR* 3.9 2.0 - - - -
93A MET* 1.3 76.0 - - - +
95A GLN* 1.3 59.1 + - - +
97A TYR* 3.8 2.4 - - - +
98A GLN* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA* 4.1 12.3 - - + +
92A THR* 3.2 38.2 + - + +
94A GLY* 1.3 74.5 - - - +
96A LEU* 1.3 59.9 + - - +
98A GLN* 3.7 12.1 - - - +
99A GLU* 2.9 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 4.1 9.9 - - + -
82A VAL* 4.3 8.3 - - + -
87A PRO* 3.9 28.0 - - + -
88A PRO* 5.6 2.0 - - + -
91A ALA* 4.9 9.6 - - + +
92A THR 3.0 17.6 + - - +
93A MET* 3.4 30.5 - - + +
95A GLN* 1.3 75.5 - - - +
97A TYR* 1.3 59.2 + - - +
99A GLU* 3.7 2.9 - - - +
100A HIS* 2.8 61.4 + - + +
107A LEU* 3.9 18.1 - - + +
109A ILE* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 3.3 37.6 + - - +
31A VAL* 3.8 28.5 - - + -
32A PRO* 4.0 12.1 - - + -
93A MET 2.9 19.0 + - - +
94A GLY 3.8 3.4 - - - +
96A LEU* 1.3 74.1 - - - +
98A GLN* 1.3 60.3 + - - +
101A HIS* 2.5 69.4 + + + +
105A PHE* 2.7 48.2 + + - +
107A LEU* 3.9 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLY 3.0 20.1 + - - +
95A GLN* 3.7 11.6 - - - +
97A TYR* 1.3 80.4 - - + +
99A GLU* 1.3 60.9 + - - +
101A HIS* 3.2 25.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLN* 2.9 22.6 + - - +
96A LEU* 5.1 2.4 - - - +
98A GLN* 1.3 80.2 - - + +
100A HIS* 1.3 92.3 + - + +
101A HIS* 3.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 3.2 34.5 - - + +
83A ASN* 2.8 34.0 + - + +
85A VAL* 5.7 6.7 - - + +
96A LEU* 2.8 39.6 + - + +
99A GLU* 1.3 112.0 + - + +
101A HIS* 1.3 65.2 - - - +
102A GLU* 3.5 1.9 + - - +
107A LEU* 3.7 11.7 - - + +
108A TYR 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU 4.1 0.2 + - - -
97A TYR* 2.5 71.1 + + + +
98A GLN* 3.2 22.4 + - + -
99A GLU 3.9 0.2 - - - -
100A HIS* 1.3 78.6 - - - +
102A GLU* 1.3 72.0 + - - +
103A GLU* 3.6 8.7 + - - +
105A PHE* 5.0 6.6 - + - -
106A PHE 3.6 6.5 - - - +
107A LEU* 4.3 5.2 - - - -
201A ZN 2.2 35.8 - - - -
----------------------------------------------------------
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