Contacts of the strand formed by residues 20 - 28 (chain A) in PDB entry 4OIN
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 TYR 20 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG 5.4 0.9 - - - -
15A THR* 3.7 5.7 - - - -
16A GLN* 3.2 64.7 + - + +
17A GLY 4.5 0.7 - - - +
18A ARG 3.8 0.2 - - - -
19A GLU* 1.3 80.9 - - + +
21A GLY* 1.3 70.1 + - - +
22A GLU* 2.6 45.4 + - + +
198A ARG* 3.2 22.5 + - + -
199A ILE 3.4 6.1 - - - -
200A TRP* 3.3 52.7 - + + -
207A PRO* 3.4 9.7 - - - +
932C GLU* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG 3.4 9.2 - - - -
15A THR* 4.4 2.0 - - - -
20A TYR* 1.3 82.2 - - - +
22A GLU* 1.3 65.4 + - - +
23A PHE* 3.8 10.8 - - - -
198A ARG* 3.4 3.6 - - - -
199A ILE 2.9 34.0 + - - -
207A PRO* 3.5 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR 4.0 0.3 - - - +
13A VAL* 3.7 1.0 - - - -
14A ARG* 2.9 77.8 + - + +
16A GLN* 5.8 0.2 + - - -
20A TYR* 2.6 40.5 + - + +
21A GLY* 1.3 74.7 - - - +
23A PHE* 1.3 68.5 + - - +
24A VAL* 4.2 1.7 - - - +
196A THR* 4.4 4.9 - - + -
197A LEU 3.3 6.3 - - - +
198A ARG* 4.3 6.0 + - - -
932C GLU* 4.3 6.8 - - - +
934C PHE* 3.3 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 4.1 9.0 - + + -
12A THR 3.5 2.9 - - - -
13A VAL* 4.0 28.0 - - + -
15A THR* 4.9 4.0 - - + -
21A GLY* 3.8 20.9 - - - -
22A GLU* 1.3 75.9 - - - +
24A VAL* 1.3 62.0 + - - +
25A LEU* 4.1 0.5 + - - +
195A LEU* 3.5 2.6 - - - +
196A THR* 3.3 2.8 - - - +
197A LEU* 2.9 52.8 + - + +
199A ILE* 3.7 24.0 - - + -
207A PRO* 3.7 9.0 - - + -
208A LEU* 3.5 50.5 - - + -
211A LEU* 3.5 28.0 - - + -
225B PHE* 5.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL 4.3 0.7 - - - +
11A PHE* 3.3 11.2 - - - -
12A THR* 2.9 47.0 + - - +
14A ARG* 3.3 40.8 - - - +
22A GLU 5.0 0.7 - - - -
23A PHE* 1.3 76.6 - - - +
25A LEU* 1.3 67.5 + - - +
26A GLU* 4.2 7.6 - - + +
194A LYS* 3.9 33.7 - - + -
195A LEU 3.2 9.0 - - - +
196A THR* 3.7 11.0 - - + +
225B PHE* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 4.3 10.5 - - + +
10A VAL 3.5 3.4 - - - +
11A PHE* 3.5 27.4 - - + -
23A PHE 5.5 0.7 - - - +
24A VAL* 1.3 71.7 - - - +
26A GLU* 1.3 62.0 + - - +
28A LEU* 3.8 21.6 - - + +
36A LEU* 3.7 29.8 - - + -
194A LYS* 3.8 1.0 - - - -
195A LEU* 2.8 40.8 + - + +
224B TYR* 3.2 43.5 - - + +
225B PHE* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 3.4 5.4 - - - +
10A VAL* 2.8 50.8 + - + +
12A THR* 6.1 0.7 - - - +
24A VAL* 4.2 7.3 - - + +
25A LEU* 1.3 77.0 - - - +
27A PRO* 1.3 74.0 - - + +
28A LEU 4.2 0.2 - - - +
184A THR* 3.1 26.3 + - - -
194A LYS* 3.5 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.8 25.3 - - + +
9A PRO* 3.2 26.9 - - + +
10A VAL* 4.7 2.0 - - + +
26A GLU* 1.3 89.7 - - + +
28A LEU* 1.3 60.9 + - - +
184A THR* 4.2 12.6 - - + +
185A ARG 5.2 2.0 - - - +
186A LEU* 4.1 26.0 - - + -
192A LEU* 3.8 22.0 - - + -
193A ASP 3.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 5.1 2.5 - - - -
9A PRO* 3.7 23.8 - - + -
25A LEU* 3.8 28.0 - - + +
27A PRO* 1.3 74.6 - - - +
29A GLU* 1.3 64.6 + - - +
32A PHE* 4.2 15.0 - - + +
33A GLY 4.6 0.4 - - - +
36A LEU* 4.2 9.4 - - + -
192A LEU* 3.4 11.3 - - - +
193A ASP* 2.7 41.7 + - + +
195A LEU* 3.8 28.9 - - + -
221B HIS* 3.6 32.8 - - + +
----------------------------------------------------------
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