Contacts of the strand formed by residues 65 - 73 (chain D) in PDB entry 5EWL
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 65 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D PRO* 4.7 14.1 - - + +
33D PRO 2.8 18.1 + - - +
34D SER* 3.2 11.6 - - - -
35D ILE* 2.8 30.7 + - - -
59D PHE* 6.5 0.9 - - + -
60D HIS* 4.8 13.9 - - + +
62D LEU 6.1 0.2 - - - +
64D VAL* 1.3 76.5 - - - +
66D PRO* 1.3 78.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ILE* 3.5 10.3 - - + +
37D ILE* 3.8 25.1 - - + -
60D HIS* 3.4 37.5 - - + +
64D VAL 4.6 1.6 - - - +
65D VAL* 1.3 96.4 - - + +
67D ARG* 1.3 60.1 + - - +
68D VAL* 3.7 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D SER* 3.9 9.9 - - - +
35D ILE 2.7 12.5 + - - +
36D GLY* 3.7 0.3 - - - -
37D ILE 3.3 10.9 + - - +
66D PRO* 1.3 71.4 - - - +
68D VAL* 1.3 56.9 + - - +
69D GLU* 2.8 27.1 - - - +
92D ARG* 3.3 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 3.3 17.3 - - + +
39D VAL* 3.7 28.5 - - + -
66D PRO* 3.7 24.2 + - + +
67D ARG* 1.3 74.7 - - - +
69D GLU* 1.3 67.5 + - - +
70D LEU* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE 3.0 15.0 + - - +
38D ALA* 3.7 5.9 - - - +
39D VAL 3.0 22.7 + - - -
67D ARG 2.8 22.2 - - - +
68D VAL* 1.3 78.1 - - - +
70D LEU* 1.3 65.9 + - - +
71D VAL* 3.5 12.0 + - + +
88D LEU* 5.8 3.5 - - - +
92D ARG* 3.1 46.7 + - + +
94D ILE* 3.6 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 3.6 21.3 - - + -
41D LEU* 3.9 24.5 - - + -
47D GLU* 3.9 29.8 - - + +
50D ILE* 3.7 29.8 - - + -
51D LYS* 4.4 20.0 - - + -
68D VAL* 4.1 15.5 - - + -
69D GLU* 1.3 71.4 - - - +
71D VAL* 1.3 62.3 + - - +
72D ALA 4.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ALA* 5.0 2.0 - - + -
39D VAL 2.8 13.2 + - - +
40D ILE* 3.4 21.8 - - + -
41D LEU* 2.8 31.3 + - - +
69D GLU* 3.9 17.0 - - + +
70D LEU* 1.3 77.6 - - - +
72D ALA* 1.3 61.5 + - - +
84D ARG* 3.4 40.2 - - + +
88D LEU* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 3.6 9.9 - - + +
43D GLY 6.0 1.3 - - - +
70D LEU 4.3 0.4 - - - -
71D VAL* 1.3 74.3 - - - +
73D MET* 1.3 60.7 + - - +
74D ASN* 4.0 9.5 - - - +
84D ARG* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ILE* 3.7 19.5 - - + -
41D LEU 3.3 7.1 + - - +
42D VAL* 3.4 28.3 - - + +
43D GLY 3.8 6.4 + - - -
71D VAL 3.9 1.2 + - - -
72D ALA* 1.3 74.1 - - - +
74D ASN* 1.3 63.1 + - - +
75D GLU 3.2 21.1 - - - +
80D SER* 4.2 4.5 - - - +
81D ILE* 3.7 28.3 - - + +
84D ARG* 3.6 37.5 - - + +
85D ILE* 5.7 0.2 - - + -
99D PHE* 3.4 38.8 - - + -
----------------------------------------------------------
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