Contacts of the strand formed by residues 70 - 77 (chain D) in PDB entry 1SMK
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 70 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLY* 4.6 0.4 - - - -
45D PHE 3.6 5.2 - - - +
47D VAL* 3.9 14.4 - - + -
64D MET* 3.7 31.9 - - + +
67D ASN* 2.8 34.5 + - + +
68D PRO* 4.2 5.7 - - - +
69D LEU* 1.3 79.9 - - - +
71D SER* 1.3 60.3 + - - +
72D VAL 3.6 21.3 - - - +
73D LEU* 4.1 9.6 - - + -
94D GLY* 4.2 1.6 - - - -
95D ALA* 3.4 34.6 + - + +
283D LEU* 3.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLY* 3.3 28.4 + - - -
45D PHE 2.9 15.2 + - - -
46D LYS* 4.1 4.7 - - - +
69D LEU 3.7 1.4 + - - -
70D VAL* 1.3 73.9 - - - +
72D VAL* 1.3 84.6 + - - +
94D GLY 4.0 3.1 - - - +
95D ALA* 3.5 2.3 - - - +
96D VAL* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D PHE 3.4 1.8 + - - +
46D LYS* 3.2 27.2 - - + +
47D VAL 2.7 32.5 + - - +
70D VAL* 3.6 3.6 - - - +
71D SER* 1.3 96.4 + - - +
73D LEU* 1.3 58.5 + - - +
74D HIS* 3.5 31.4 - - + +
96D VAL* 3.6 14.8 - - + +
98D ARG* 5.9 2.0 - - - -
113D MET* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 3.2 21.5 - - + +
49D ILE* 3.8 28.5 - - + -
61D ALA 3.7 11.4 - - - +
64D MET* 4.1 9.0 - - + -
65D LYS* 3.7 40.4 - - + +
70D VAL* 4.1 9.2 - - + -
72D VAL* 1.3 74.2 - - - +
74D HIS* 1.3 63.1 + - - +
75D LEU* 3.8 17.3 - - + -
88D ILE* 4.8 1.6 - - + -
95D ALA* 4.6 4.9 - - + -
96D VAL 3.0 11.0 + - - +
97D VAL* 3.2 11.1 - - + +
98D ARG 3.1 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL 2.8 12.2 + - - +
48D ALA* 3.3 6.2 - - + +
49D ILE 2.8 28.9 + - - -
72D VAL* 3.5 22.2 - - + +
73D LEU* 1.3 80.6 - - - +
75D LEU* 1.3 63.3 + - - +
76D TYR* 3.7 1.7 + - - +
98D ARG* 3.6 24.9 + - + -
100D PHE* 3.1 36.5 - + + -
108D ALA 3.8 7.6 - - - -
109D ALA* 2.8 28.6 + - + +
111D THR 4.6 3.6 - - - -
113D MET* 3.5 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ILE* 4.0 7.4 - - + -
52D ALA* 3.7 15.0 - - + -
61D ALA* 3.5 22.7 - - + -
73D LEU* 3.8 20.6 - - + -
74D HIS* 1.3 74.1 - - - +
76D TYR* 1.3 59.9 + - - +
81D ALA* 4.3 6.5 - - + +
84D VAL* 4.0 14.4 - - + -
85D THR* 4.0 19.3 - - - +
88D ILE* 3.5 28.3 - - + -
97D VAL* 3.7 24.2 - - + -
98D ARG 2.8 12.0 + - - +
99D GLY* 3.4 2.1 - - - -
100D PHE* 2.9 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ALA* 6.4 0.2 - - + -
49D ILE 3.0 7.4 + - - +
50D LEU* 3.7 34.8 - - + -
51D GLY 2.8 30.4 + - - -
52D ALA* 3.1 5.5 + - - -
74D HIS 3.7 2.1 + - - +
75D LEU* 1.3 75.0 - - - +
77D ASP* 1.3 73.0 + - - +
78D VAL* 4.3 13.4 - - + +
100D PHE* 3.3 28.5 - - + -
102D GLY* 3.1 32.0 - - - -
103D GLN* 3.3 23.2 + - - +
106D LEU* 3.8 26.4 - - + +
109D ALA* 4.0 13.5 - - + -
144D LEU* 4.3 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D GLY* 2.8 22.9 - - - +
52D ALA* 5.2 0.2 - - + -
53D ALA* 2.7 40.9 + - + +
54D GLY* 3.7 3.1 + - - -
76D TYR* 1.3 87.6 - - - +
78D VAL* 1.3 82.9 + - - +
79D VAL* 3.5 18.5 + - - +
81D ALA* 4.3 6.5 - - + +
100D PHE 3.1 7.8 + - - +
101D LEU* 3.6 2.8 - - - -
102D GLY 3.0 23.4 + - - -
----------------------------------------------------------
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