Contacts of the strand formed by residues 11 - 17 (chain I) in PDB entry 3SDI
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 CYS 11 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I GLY* 2.9 33.3 + - - +
9I LYS 3.4 13.5 - - - +
10I ASP* 1.3 79.4 - - - +
12I VAL* 1.3 70.4 + - - +
104I ILE* 3.9 3.6 - - - -
108I PRO* 3.7 7.0 - - - +
146I LEU 3.8 8.1 - - - -
148I PRO* 4.0 27.1 - - + -
151I LEU* 3.7 22.2 - - + -
177I ILE* 5.2 1.3 - - + -
178I ILE 3.2 17.9 - - - +
179I LYS* 4.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I MET 3.3 9.2 - - - +
7I THR* 3.9 13.2 - - + -
11I CYS* 1.3 80.7 - - - +
13I ALA* 1.3 61.1 + - - +
102I ALA* 4.2 3.8 - - + -
103I GLY* 3.8 26.0 - - - +
104I ILE* 4.4 2.0 - - + +
108I PRO* 3.6 20.2 - - + -
109I PHE 3.8 17.9 - - - +
110I ILE* 4.4 5.8 - - + -
151I LEU* 3.9 4.8 - - - +
177I ILE* 3.9 1.2 - - - +
178I ILE* 2.9 57.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ALA* 3.1 6.2 - - - +
6I MET 2.8 35.8 + - - +
12I VAL* 1.3 75.7 - - - +
14I ILE* 1.3 61.5 + - - +
102I ALA* 4.7 1.3 - - - +
151I LEU* 3.7 22.2 - - + +
155I ILE* 3.8 21.5 - - + -
175I VAL* 5.0 0.2 - - + -
176I TYR 3.2 12.8 - - - +
177I ILE* 3.8 13.7 - - + -
178I ILE* 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I VAL* 4.1 8.7 - - + -
4I VAL 3.3 11.9 - - - +
5I ALA* 4.0 5.4 - - + -
13I ALA* 1.3 75.2 - - - +
15I ALA* 1.3 63.3 + - - +
34I ILE* 3.6 30.4 - - + +
42I PHE* 4.2 7.9 - - + -
43I LEU 4.5 1.1 - - - -
44I GLY* 3.7 31.2 - - - +
100I VAL* 3.9 14.4 - - + +
102I ALA* 4.1 17.0 - - + +
155I ILE* 4.1 1.3 - - - -
175I VAL* 4.6 0.4 - - - -
176I TYR* 2.8 46.4 + - + +
178I ILE* 4.0 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I VAL* 3.2 6.8 - - - +
4I VAL* 2.8 33.8 + - + +
14I ILE* 1.3 74.9 - - - +
16I CYS* 1.3 62.3 + - - +
34I ILE* 3.6 4.3 - - - -
155I ILE* 3.9 18.4 - - + +
159I LEU* 4.1 19.3 - - + -
174I VAL 3.2 12.1 - - - +
175I VAL* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 16 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I ILE 3.2 14.4 - - - +
3I VAL* 3.7 13.9 - - + -
15I ALA* 1.3 76.8 - - - +
17I ASP* 1.3 71.2 + - - +
18I LEU* 4.6 0.7 - - - -
32I GLU* 4.4 3.6 - - - -
33I LYS* 3.6 25.8 - - + -
34I ILE* 3.8 11.2 - - + -
159I LEU* 4.0 8.2 - - - +
173I ALA* 3.3 4.9 - - - +
174I VAL* 2.9 53.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 17 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I GLY* 3.2 12.2 - - - -
2I ILE* 2.8 43.8 + - + +
16I CYS* 1.3 87.8 - - - +
18I LEU* 1.3 62.4 + - - +
19I ARG* 3.6 7.8 - - - +
31I PHE 3.5 1.6 - - - +
33I LYS* 3.0 20.2 + - - -
159I LEU* 4.3 2.5 - - + +
163I ALA* 5.5 0.9 - - + -
169I SER* 3.4 9.5 - - - -
170I GLY* 2.9 38.6 + - - +
172I GLY 3.3 8.5 - - - +
173I ALA* 4.1 3.4 - - + +
191I MET* 5.6 0.2 - - - -
----------------------------------------------------------
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