Contacts of the strand formed by residues 2 - 8 (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 ILE 2 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I GLY* 1.3 78.9 - - - +
3I VAL* 1.3 66.1 + - - +
16I CYS* 3.2 23.0 - - - +
17I ASP* 2.8 26.2 + - + +
33I LYS* 4.4 0.7 - - - +
46I THR* 3.5 2.1 - - - +
127I SER 3.3 12.8 - - - +
129I THR 4.1 0.2 - - - +
130I ALA* 3.5 33.2 - - + +
134I LEU* 3.9 18.2 - - + -
159I LEU* 3.8 27.6 - - + +
163I ALA* 3.8 34.8 - - + +
169I SER* 3.6 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 3 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I ILE* 1.3 80.1 - - - +
4I VAL* 1.3 67.0 + - - +
14I ILE* 4.1 11.4 - - + -
15I ALA 3.2 9.2 - - - +
16I CYS* 3.7 15.3 - - + -
33I LYS* 4.1 6.7 - - + -
34I ILE* 4.9 0.4 - - + -
44I GLY* 4.0 13.7 - - - -
45I ILE 4.1 16.8 - - - +
46I THR* 3.5 19.2 - - + +
100I VAL* 3.8 32.3 - - + +
126I VAL* 3.7 1.0 - - - -
127I SER* 2.9 31.7 + - - +
134I LEU* 3.8 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 4 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I VAL* 1.3 77.9 - - - +
5I ALA* 1.3 70.5 + - - +
6I MET* 4.5 2.5 - - + -
14I ILE* 3.3 4.1 - - - +
15I ALA* 2.8 38.5 + - + +
100I VAL* 5.4 0.2 - - - -
124I PHE* 5.1 0.2 - - + -
125I ILE 3.3 11.7 - - - +
126I VAL* 4.2 3.1 - - + -
134I LEU* 4.0 18.2 - - + -
138I CYS* 4.0 26.2 - - - -
155I ILE* 3.6 20.8 - - + +
158I ALA* 5.4 0.9 - - + -
159I LEU* 3.8 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 5 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I VAL* 1.3 76.9 - - - +
6I MET* 1.3 63.9 + - - +
13I ALA 3.1 12.6 - - - +
14I ILE* 4.0 9.9 - - + -
100I VAL* 3.6 24.6 - - + +
102I ALA* 4.3 4.0 - - + -
110I ILE* 3.9 20.6 - - + +
124I PHE* 3.1 6.9 - - - +
125I ILE* 2.9 32.1 + - + +
155I ILE* 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 6 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I VAL* 4.5 1.6 - - + -
5I ALA* 1.3 77.8 - - - +
7I THR* 1.3 62.3 - - - +
12I VAL* 3.3 5.2 - - - +
13I ALA* 2.8 37.7 + - + +
110I ILE* 4.4 2.6 - - - +
123I ASP 3.3 8.3 - - - +
124I PHE* 4.0 9.0 - - + -
138I CYS* 3.8 32.8 - - + -
142I TYR* 3.5 26.2 - - + -
151I LEU* 3.7 21.2 - - + +
154I THR* 3.9 21.3 - - + -
155I ILE* 3.7 38.8 - - + -
158I ALA* 4.1 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I MET* 1.3 77.8 - - - +
8I GLY* 1.3 60.7 + - - +
11I CYS 3.8 5.8 - - - -
12I VAL* 3.9 16.6 - - + -
108I PRO* 4.3 13.7 - - + +
109I PHE 4.6 4.3 - - - +
110I ILE* 4.0 19.1 - - + +
122I LYS* 2.6 32.4 + - - +
123I ASP 3.1 3.3 + - - -
142I TYR* 2.9 31.5 + - - -
143I GLU 5.1 1.0 - - - +
145I ASN 5.2 0.2 + - - -
146I LEU* 5.2 0.3 + - - +
151I LEU* 3.6 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 8 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I THR* 1.3 74.7 - - - +
9I LYS* 1.3 60.6 + - - -
10I ASP 3.2 7.3 + - - -
11I CYS* 2.9 22.4 + - - +
108I PRO* 4.2 7.6 - - - +
145I ASN* 4.2 10.3 + - - -
146I LEU* 3.5 20.0 - - - -
151I LEU* 4.1 4.6 - - - +
----------------------------------------------------------
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