Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 2WMH
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 LEU 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 4.3 15.9 - - + -
40A THR 5.9 0.2 - - - +
41A ILE* 3.9 29.6 - - + +
46A PRO* 1.3 74.9 - - - +
48A LEU* 1.3 64.0 + - - +
49A LEU* 4.2 12.6 - - + -
81A TYR* 3.3 14.4 - - - +
82A ALA* 3.9 20.4 - - - +
83A ALA* 4.1 10.1 - - + +
124A PHE* 4.0 23.8 - - + -
186A ILE* 4.5 3.8 - - + -
296A THR 2.9 12.8 + - - +
297A VAL* 3.4 19.1 - - + +
298A TYR* 2.9 29.6 + - - +
325A PHE* 3.8 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 1.3 71.7 - - - +
49A LEU* 1.3 65.2 + - - +
50A SER* 4.1 9.0 + - - +
74A ILE* 5.1 1.6 - - + -
78A VAL* 3.9 13.7 - - + -
81A TYR 2.8 10.3 + - - +
82A ALA* 3.3 7.7 - - + +
83A ALA 3.0 26.2 + - - +
287A MET* 5.2 0.2 - - + -
298A TYR* 3.6 6.7 - - + +
300A PHE* 3.6 31.4 - - + -
317A PHE* 4.2 15.3 - - + -
321A ILE* 3.8 12.6 - - + -
322A ILE* 3.9 28.0 - - + -
325A PHE* 3.4 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.2 9.4 - - + -
48A LEU* 1.3 74.3 - - - +
50A SER* 1.3 63.2 + - - +
51A PRO* 4.4 0.3 - - - +
83A ALA* 3.5 17.9 - - + +
85A GLU* 4.8 9.4 - - + +
124A PHE* 3.6 36.8 - - + -
155A LEU* 4.3 8.7 - - + -
186A ILE* 3.9 24.7 - - + -
188A HIS* 4.7 1.3 - - - +
297A VAL* 4.2 15.0 - - + -
298A TYR 2.8 15.9 + - - +
299A ASN* 3.6 44.1 - - + +
300A PHE* 4.0 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.3 6.6 + - - +
49A LEU* 1.3 75.1 + - - +
51A PRO* 1.4 66.2 - - - +
74A ILE* 3.7 10.5 - - - +
83A ALA 3.2 7.3 + - - -
84A ILE* 3.4 19.6 - - - +
85A GLU* 2.9 20.4 + - - -
307A PHE* 3.6 32.8 - - - -
317A PHE* 3.7 21.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU 4.4 3.4 - - - +
50A SER* 1.4 84.5 - - - +
52A LEU* 1.3 62.0 + - - +
53A TYR* 3.7 15.4 - - + +
63A TRP* 5.9 0.5 - - - -
65A ASN* 5.3 1.6 + - - -
85A GLU* 3.5 34.3 - - + +
299A ASN* 4.6 3.8 - - - +
300A PHE* 3.5 27.8 - - + +
301A GLU* 5.5 0.4 - - + -
303A ALA* 3.7 28.2 - - + +
306A THR* 5.5 0.2 - - - +
307A PHE* 3.4 25.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO* 1.3 78.0 - - - +
53A TYR* 1.3 67.8 + - - +
61A LEU* 4.0 20.9 - - + -
62A TRP 5.6 0.4 - - - +
63A TRP* 6.2 0.4 - - - -
65A ASN* 3.5 37.7 - - + +
66A THR 3.9 3.1 - - - +
67A LEU* 3.7 40.6 - - + +
70A ALA* 3.7 24.2 - - + -
84A ILE* 3.7 13.5 - - + -
85A GLU 2.8 10.9 + - - +
86A LEU* 3.7 8.0 - - + -
87A HIS* 2.9 26.0 + - - +
108A TRP* 5.0 0.2 - - - -
307A PHE* 4.4 1.6 - - + -
308A MET* 4.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO* 3.7 28.7 - - + -
52A LEU* 1.3 82.7 - - - +
54A GLY* 1.3 57.9 + - - +
61A LEU* 3.2 8.9 - - - +
62A TRP* 2.7 43.1 + - + +
63A TRP* 3.7 31.8 - + + -
85A GLU* 4.1 3.2 + - - -
87A HIS* 3.3 26.2 - + + -
89A ALA* 3.5 15.0 - - + -
97A CYS* 4.5 0.7 - - - -
108A TRP* 4.5 0.2 - - - -
301A GLU* 3.3 22.9 + - + +
303A ALA* 5.0 2.2 - - + -
512A TRP* 3.4 30.3 - + + -
2B FUC 2.8 34.3 + - - -
----------------------------------------------------------
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