Contacts of the strand formed by residues 37 - 45 (chain D) in PDB entry 2Y05
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 VAL 37 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.4 7.9 - - - +
35D GLY 5.0 0.2 - - - +
36D GLU* 1.3 81.1 - - - +
38D LEU* 1.3 59.1 + - - +
39D LEU* 3.9 21.3 - - + -
71D VAL* 4.0 10.3 - - + -
73D GLU 3.5 7.6 - - - +
74D SER* 3.7 19.3 - - - +
76D ASN* 4.0 4.3 - - + -
79D LEU* 3.7 31.6 - - + +
95D SER 3.8 0.2 - - - +
96D ILE* 3.4 6.4 - - - -
97D SER* 2.9 49.4 + - - +
102D LEU* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SER* 3.9 27.8 - - - +
29D LEU* 4.0 17.0 - - + -
32D LEU* 3.5 11.4 - - + +
37D VAL* 1.3 71.8 - - - +
39D LEU* 1.3 61.3 + - - +
71D VAL* 3.5 5.2 - - - -
72D VAL* 3.0 45.9 + - + +
73D GLU* 2.9 28.0 + - + +
94D HIS* 4.3 18.4 - - + -
95D SER 3.6 14.6 - - - +
96D ILE* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 3.9 14.4 - - + +
38D LEU* 1.3 72.9 - - - +
40D GLU* 1.3 59.0 + - - +
41D ALA 4.1 0.4 + - - -
67D GLN* 5.0 1.9 - - - +
69D ALA* 4.0 9.4 - - + -
70D LYS 3.5 3.1 - - - +
71D VAL* 3.6 32.3 - - + +
72D VAL* 4.5 2.0 - - - -
85D VAL* 3.8 18.2 - - + -
87D ALA* 3.9 15.9 - - + -
94D HIS* 3.2 10.4 - - - +
95D SER* 2.8 50.6 + - - +
97D SER* 4.0 11.2 - - - -
102D LEU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU 4.2 0.4 + - - -
39D LEU* 1.3 73.9 - - - +
41D ALA* 1.3 73.9 + - - +
42D LEU* 3.4 12.9 + - + +
69D ALA* 3.3 3.3 - - - -
70D LYS* 2.8 36.2 + - + +
72D VAL* 3.8 30.3 - - + +
93D THR 3.7 2.5 - - - +
94D HIS* 2.8 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLU* 1.3 80.3 - - - +
42D LEU* 1.3 61.3 + - - +
44D LEU* 4.2 17.9 - - + -
67D GLN* 3.5 27.3 + - - +
68D VAL 3.9 3.4 - - - +
92D THR 3.7 13.0 - - - +
93D THR* 2.9 23.8 + - - +
329D ALA* 3.5 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLU* 4.0 19.5 - - - +
41D ALA* 1.3 78.7 - - - +
43D PHE* 1.3 80.4 + - + +
68D VAL* 2.8 22.4 + - + +
70D LYS* 4.2 20.9 - - + +
84D ILE* 4.1 17.5 - - + -
115D LEU* 3.9 27.6 - - + -
328D LYS* 3.8 3.8 - - - +
329D ALA* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 1.3 97.3 - - + +
44D LEU* 1.3 62.5 + - - +
67D GLN* 3.2 4.2 - - - +
68D VAL* 2.8 40.7 + - + -
114D PRO* 5.7 3.4 - - + -
115D LEU* 4.3 23.3 - - + -
116D SER* 3.8 27.4 - - - -
119D LEU* 3.4 15.9 - - + +
302D ILE* 5.1 8.7 - - + -
326D ILE* 3.7 21.3 - - + -
327D VAL 3.3 4.9 - - - +
328D LYS* 3.8 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ALA* 4.2 13.7 - - + -
43D PHE* 1.3 78.2 - - - +
45D THR* 1.3 62.0 + - - +
66D GLN 3.9 7.9 - - - +
67D GLN* 3.6 28.0 - - + +
90D GLY 4.3 3.4 - - - +
92D THR 3.8 15.9 - - - +
119D LEU* 3.9 4.0 - - - -
306D PHE* 4.0 23.3 - - + -
309D MET* 3.6 33.0 - - + -
326D ILE* 3.6 3.6 - - - +
327D VAL* 2.7 59.0 + - + +
329D ALA* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 1.3 73.5 - - - +
46D VAL* 1.3 60.1 + - - +
47D ASP* 2.7 22.9 + - - +
50D MET* 3.5 10.4 - - - +
65D GLY* 5.1 0.3 - - - -
66D GLN* 3.3 40.8 + - + +
91D TRP* 4.7 0.2 + - - -
119D LEU* 3.8 21.4 - - + +
309D MET* 3.5 14.6 - - - +
324D LYS* 2.7 36.6 + - - -
325D THR 4.2 4.7 - - - -
326D ILE* 4.5 0.9 - - - -
----------------------------------------------------------
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