Contacts of the helix formed by residues 90 - 99 (chain A) in PDB entry 3W31
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 TYR 90 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.9 18.4 - - + -
87A ILE 3.3 1.2 + - - -
89A GLU* 1.3 78.3 - - - +
91A MET* 1.3 65.9 + - + +
92A THR* 3.2 2.9 - - - -
93A GLY* 2.8 22.3 + - - +
94A PHE* 3.2 19.6 + + + -
97A ARG* 4.2 9.4 + - - -
196A GLU* 2.7 37.9 + - - -
199A HIS* 3.0 35.5 - + - -
200A TYR* 3.2 55.0 - + + +
203A SER* 4.1 14.4 - - - -
205A SER* 4.0 8.0 + - - +
301A IOD 4.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER* 3.7 29.8 - - - +
64A GLY* 4.1 12.8 - - - -
67A LEU* 3.6 32.5 - - + -
82A PRO* 5.5 5.8 - - + -
87A ILE* 3.0 49.8 + - + +
90A TYR* 1.3 82.3 - - + +
92A THR* 1.3 60.5 + - - +
94A PHE* 3.7 25.7 - - + +
95A PHE* 3.0 25.3 + - - +
137A MET* 4.9 1.1 - - + -
200A TYR* 5.6 3.1 - - - -
96B SER* 4.2 1.3 - - - -
98B ALA* 3.9 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE 3.8 1.4 + - - -
88A SER* 2.8 36.3 - - - +
89A GLU 4.9 1.3 - - - +
90A TYR 4.4 1.6 - - - +
91A MET* 1.3 79.3 - - - +
93A GLY* 1.3 61.2 + - - +
95A PHE* 3.7 2.6 - - - +
96A HIS* 3.0 34.5 + - + +
95B TRP 5.0 1.7 + - - -
96B SER* 3.3 21.6 + - - -
97B PRO* 3.5 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR 2.8 8.6 + - - -
92A THR* 1.3 82.1 - - - +
94A PHE* 1.3 56.6 + - - +
95A PHE 3.1 1.3 - - - -
96A HIS* 2.6 35.5 - - - +
97A ARG* 2.7 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.4 20.2 - - + -
90A TYR* 3.2 17.4 + + + +
91A MET* 3.7 25.6 - - + +
93A GLY* 1.3 73.9 - - - +
95A PHE* 1.3 68.0 + + + +
97A ARG* 3.3 13.4 - - - +
98A HIS* 2.9 64.6 + + + +
102A ILE* 5.2 0.2 - - + -
137A MET* 3.7 33.7 - - + -
146A TRP* 3.8 28.7 - + - -
190A ILE* 4.4 2.0 - - + -
192A VAL* 4.1 18.8 - - + -
196A GLU* 4.3 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET 3.0 15.9 + - - +
92A THR 3.7 5.2 - - - +
94A PHE* 1.3 78.8 - + - +
96A HIS* 1.3 70.4 + - - +
97A ARG 2.9 0.3 + - - -
99A LEU* 2.9 35.5 + - + +
102A ILE* 4.1 21.8 - - + -
143A ALA* 3.3 35.4 - - + -
146A TRP* 4.2 10.3 - + - -
4B LEU* 4.2 18.8 - - + -
7B ARG* 4.2 1.8 - - - -
63B PRO* 5.0 0.7 - - + -
64B MET* 3.2 35.0 - - + -
97B PRO* 3.8 35.7 - - + -
98B ALA* 4.4 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 3.0 20.0 + - + +
93A GLY* 2.6 25.6 - - - +
95A PHE* 1.3 79.2 - - - +
97A ARG* 1.3 67.3 + - + +
99A LEU* 3.6 10.6 - - - +
64B MET* 4.5 16.8 - - + +
97B PRO* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 4.2 24.0 + - - -
93A GLY* 2.7 27.7 + - - -
94A PHE* 3.3 24.0 - - - +
95A PHE 2.9 0.2 + - - -
96A HIS* 1.3 78.4 + - + +
98A HIS* 1.3 60.7 + - + +
99A LEU* 2.6 19.8 + - - +
100A GLU* 4.1 5.2 + - - +
196A GLU* 2.5 30.5 + - - -
199A HIS* 4.6 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 2.9 44.0 + + + +
95A PHE 3.7 1.6 - - - -
97A ARG* 1.3 77.4 - - + +
99A LEU* 1.3 63.6 + - - -
100A GLU 3.2 1.8 - - - -
101A GLN* 3.1 24.6 + - - +
102A ILE* 3.5 17.4 + - + +
190A ILE* 3.7 31.2 - - + -
191A HIS 3.8 13.2 + - - -
192A VAL* 3.9 13.3 - - + +
193A SER* 4.7 1.6 + - - -
196A GLU* 3.3 43.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PHE* 2.9 24.2 + - + +
96A HIS 3.6 9.4 - - - +
97A ARG 2.6 9.2 + - - +
98A HIS* 1.3 74.5 - - - +
100A GLU* 1.3 84.0 + - + +
102A ILE* 3.0 12.0 + - + +
103A ASP* 2.9 37.0 + - + +
4B LEU* 6.0 4.5 - - + -
64B MET* 3.7 33.4 - - + -
----------------------------------------------------------
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