Contacts of the strand formed by residues 205 - 212 (chain A) in PDB entry 2WFK
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 GLY 205 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 3.6 14.1 - - - -
44A VAL* 2.9 30.7 + - - +
105A GLU 4.7 0.2 - - - -
110A HIS* 4.4 7.0 - - - -
111A TRP* 4.3 11.0 - - - -
112A PHE* 3.5 14.2 - - - -
204A LYS* 1.3 78.2 - - - +
206A SER* 1.3 64.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY 3.5 12.1 - - - -
43A TYR* 3.5 15.5 - - - -
80A SER* 2.9 25.2 + - - -
81A PRO* 3.5 4.9 - - - +
82A THR* 2.9 37.7 + - - -
98A PHE* 4.3 2.7 - - - -
105A GLU 4.6 2.0 + - - -
106A LYS* 3.1 25.3 + - - -
110A HIS 4.8 2.4 + - - -
112A PHE* 4.0 0.5 - - - -
205A GLY* 1.3 72.8 - - - -
207A PHE* 1.3 64.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 4.1 31.0 - + - -
41A TYR* 3.6 2.9 - - - -
42A GLY* 3.0 59.3 + - - +
43A TYR 4.0 2.7 - - - -
44A VAL* 4.0 17.9 - - + -
61A TYR* 4.3 23.8 - + + -
78A MSE 3.5 35.7 - - + -
79A ILE 3.1 14.6 - - - +
80A SER* 4.2 1.8 - - - -
82A THR* 3.4 11.5 - - - +
112A PHE* 3.8 15.3 - + + -
195A PHE* 4.4 4.0 - - + -
206A SER* 1.3 77.2 - - - +
208A VAL* 1.3 67.6 + - - +
209A ALA* 4.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.9 32.8 - - + -
39A ASN* 4.6 1.3 - - + -
40A TYR 3.3 5.2 - - - +
41A TYR* 3.7 35.0 - - + -
77A ARG* 4.0 2.3 - - - +
78A MSE 3.5 1.7 - - - -
79A ILE* 2.9 55.4 + - + +
82A THR* 3.8 17.3 - - + -
85A ILE* 5.0 6.5 - - + -
207A PHE* 1.3 77.2 - - - +
209A ALA* 1.3 70.3 + - - +
210A SER* 4.2 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE 3.7 0.6 - - - +
39A ASN* 3.2 5.7 - - - +
40A TYR* 2.7 54.2 + - + +
63A LEU* 5.1 0.4 - - + -
77A ARG 3.3 5.4 - - - -
78A MSE 4.5 0.7 - - + +
195A PHE* 3.4 44.9 - - + -
207A PHE* 4.1 6.7 - - + -
208A VAL* 1.3 74.0 - - - +
210A SER* 1.3 62.3 + - - +
211A VAL* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.1 4.0 - - - +
10A LEU* 3.7 19.1 - - - -
37A VAL* 4.9 1.6 - - - -
38A ILE 3.3 5.2 - - - -
39A ASN* 2.7 23.4 + - - -
75A GLY 3.6 0.2 - - - +
76A VAL* 3.4 6.8 - - - +
77A ARG* 2.9 64.7 + - - +
208A VAL* 4.2 1.9 + - - +
209A ALA* 1.3 75.0 + - - +
211A VAL* 1.3 65.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.2 2.9 - - - -
36A SER 3.8 0.9 - - - +
37A VAL* 3.2 4.3 - - - +
38A ILE* 2.9 43.8 + - + +
63A LEU* 3.8 25.1 - - + -
65A VAL* 4.6 2.2 - - + -
74A MSE 4.6 5.6 - - + -
75A GLY 3.3 7.0 - - - +
76A VAL* 4.8 1.1 - - + -
193A ILE* 3.7 33.2 - - + -
195A PHE* 4.0 8.7 - - + -
210A SER* 1.3 79.6 - - - +
212A GLY* 1.3 67.3 + - - +
213A LEU* 4.5 5.2 - - + -
226A ILE* 3.7 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.9 2.2 - - - +
34A TYR* 3.5 26.2 - - - -
36A SER 3.3 7.9 - - - -
37A VAL* 4.1 3.6 - - - -
74A MSE 3.3 5.7 - - - +
75A GLY 2.8 33.2 + - - -
211A VAL* 1.3 74.6 - - - +
213A LEU* 1.3 67.8 + - - +
----------------------------------------------------------
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