Contacts of the strand formed by residues 5 - 14 (chain C) in PDB entry 3SHD
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 HIS 5 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LYS 4.7 0.4 - - - -
4C PRO* 1.3 74.3 - - + +
6C VAL* 1.3 60.8 + - - +
7C THR 4.0 0.2 - - - -
37C HIS* 3.2 27.5 + + + +
77C THR* 3.4 32.3 - - + +
78C PRO* 3.1 21.2 + - + +
79C PHE* 3.1 17.8 - - + -
80C LEU 2.7 26.0 + - - +
1G MET* 3.8 24.8 - - + -
2G PHE 6.0 0.2 - - - -
3G LYS* 3.1 32.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 6 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO* 3.6 7.4 + - + +
5C HIS* 1.3 77.0 - - - +
7C THR* 1.3 57.9 + - - +
37C HIS* 3.5 6.5 - - - +
38C LEU* 2.7 41.3 + - + +
44C LEU* 4.1 13.2 - - + -
80C LEU* 3.2 17.0 - - + +
82C PHE* 3.3 35.2 - - + -
2G PHE 5.8 1.0 + - - -
3G LYS* 5.6 1.6 - - - +
4G PRO* 3.7 31.0 - - + +
6G VAL* 4.7 0.4 - - + -
80G LEU* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C HIS 4.0 0.4 - - - -
6C VAL* 1.3 73.5 - - - +
8C VAL* 1.3 68.9 + - - +
36C GLY* 3.2 10.1 - - - -
37C HIS* 3.5 50.0 - - + +
38C LEU 4.1 0.7 - - - +
79C PHE* 3.8 14.9 - - + -
80C LEU 2.8 14.3 + - - +
81C ARG* 3.7 9.6 - - - +
82C PHE* 3.1 25.8 + - - -
158C SO4 2.6 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C THR* 1.3 81.1 - - - +
9C ALA* 1.3 61.9 + - - +
35C ALA* 2.8 21.4 - - - +
36C GLY 2.8 28.7 + - - +
37C HIS 5.4 0.2 - - - -
38C LEU 5.6 1.6 - - - +
44C LEU* 3.6 40.4 - - + +
47C ALA* 3.7 15.3 - - + +
48C ALA* 3.6 28.0 - - + +
51C GLU* 4.8 2.2 - - + -
81C ARG* 5.0 1.3 - - - -
82C PHE* 3.3 7.6 - - + +
84C PHE* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 1.3 77.2 - - - +
10C CYS* 1.3 61.6 + - - +
33C GLN* 4.3 1.6 - - + -
34C PRO 3.6 0.9 - - - +
35C ALA* 3.4 19.1 - - + -
81C ARG* 3.5 34.1 - - - +
82C PHE 2.8 7.8 + - - +
83C LEU* 3.4 12.1 - - + -
84C PHE* 2.8 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 1.3 80.5 - - - +
11C VAL* 1.3 64.6 + - - +
12C VAL* 3.6 21.1 + - + -
19C LEU 5.2 0.2 - - - +
33C GLN* 3.1 21.4 - - - +
34C PRO* 3.0 21.3 + - + +
48C ALA* 4.0 35.4 - - - -
52C LEU* 4.7 9.6 - - + -
62C PRO* 4.6 4.0 - - - -
84C PHE* 3.3 8.7 - - - +
86C ILE* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C CYS* 1.3 73.7 - - - +
12C VAL* 1.3 61.4 + - - +
13C HIS 3.9 0.3 + - - -
18C PHE* 3.7 22.7 - - + -
33C GLN* 3.9 20.0 - - + +
66C ILE* 4.3 4.5 - - + -
83C LEU* 4.1 16.8 - - + -
84C PHE 2.6 14.7 + - - +
85C ALA* 3.5 0.9 - - - +
86C ILE 2.8 29.3 + - - +
126C SER* 4.0 22.0 - - - +
127C ILE* 5.0 4.0 - - + -
130C TYR* 3.3 37.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C CYS* 3.6 24.4 + - + +
11C VAL* 1.3 78.6 - - - +
13C HIS* 1.3 60.3 + - - +
18C PHE* 3.2 8.2 - - - +
19C LEU* 2.8 50.5 + - + +
34C PRO* 4.9 2.7 - - + -
52C LEU* 4.5 18.8 - - + -
58C ILE* 5.4 0.2 - - + -
86C ILE* 3.3 20.2 - - + +
88C LEU* 3.3 35.2 - - + -
106C TRP* 3.7 10.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 1.3 73.7 - - - +
14C ALA* 1.3 64.1 + - - +
15C GLU 4.7 0.7 - - - -
16C GLY* 3.4 39.2 + - - -
17C LYS 3.2 12.4 + - - -
18C PHE* 3.4 26.8 - + + -
86C ILE 3.0 5.3 + - - -
87C GLU* 3.0 31.5 - - - +
88C LEU 2.8 28.3 + - - +
106C TRP* 4.1 1.1 - - - -
130C TYR* 3.1 28.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C HIS* 1.3 76.8 - - - +
15C GLU* 1.3 72.6 + - - +
16C GLY 3.4 1.6 - - - -
17C LYS 3.0 15.7 + - - +
88C LEU* 3.6 22.2 - - + +
90C GLN* 3.6 29.4 - - - +
91C ILE* 3.3 18.0 - - + +
106C TRP* 3.5 10.9 - - + -
----------------------------------------------------------
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