Contacts of the strand formed by residues 31 - 38 (chain A) in PDB entry 1ML3
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 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 4.7 1.8 - - - -
3A ILE* 3.5 20.2 - - + +
5A VAL* 3.6 27.6 - - + -
21A LEU* 3.4 33.7 - - + -
26A LEU* 2.7 33.3 + - + +
27A LEU* 3.5 4.9 - - - +
28A GLY* 2.9 25.3 + - - -
30A GLU* 1.3 83.4 - - + +
32A ASP* 1.3 63.8 - - - +
33A VAL 3.6 4.4 + - - +
344A VAL* 4.1 6.3 - - + -
347A VAL* 5.0 10.3 - - + -
348A ARG* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 4.3 14.6 - - + +
3A ILE 2.6 15.8 + - - +
4A LYS* 3.1 33.1 - - + +
5A VAL 2.9 20.0 + - - -
28A GLY* 4.8 2.0 - - - +
31A ILE* 1.3 71.9 - - - +
33A VAL* 1.3 58.8 + - - +
34A VAL* 2.9 20.5 + - - +
83A HIS* 2.7 34.0 + - - +
84A ARG 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 3.3 15.9 - - + +
7A ILE* 4.5 10.5 - - + -
18A PHE* 4.3 15.5 - - + -
21A LEU* 3.8 38.6 - - + -
27A LEU* 4.1 10.1 - - + +
31A ILE* 3.6 7.1 + - + -
32A ASP* 1.3 70.6 + - - +
34A VAL* 1.3 60.4 + - - +
35A ALA 3.9 18.2 - - - +
36A VAL* 4.3 7.0 - - + -
83A HIS* 2.8 23.4 - - - -
85A ILE* 3.5 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 3.9 19.3 - - + -
5A VAL 2.9 10.8 + - - +
32A ASP* 2.9 33.3 + - - +
33A VAL* 1.3 72.5 - - - +
35A ALA* 1.3 57.6 - - - +
83A HIS* 5.0 0.4 - - - -
84A ARG 4.1 3.4 - - - +
85A ILE* 3.8 2.4 - - - -
86A LEU* 3.2 24.1 + - + +
102A LEU* 3.9 36.3 - - + +
104A VAL* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL 3.9 2.0 + - - -
6A GLY* 3.5 4.8 - - - -
7A ILE 3.1 21.3 + - - -
33A VAL* 3.6 4.6 - - - +
34A VAL* 1.3 82.1 - - + +
36A VAL* 1.3 71.1 + - - +
37A VAL 4.3 0.2 - - - -
85A ILE* 4.1 2.0 - - - -
86A LEU* 3.2 15.5 - - + +
88A VAL* 3.9 10.3 - - + -
99A TRP* 4.6 10.8 - - + -
102A LEU* 3.6 30.1 - - + -
104A VAL* 4.9 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.2 18.2 - - + +
10A PHE* 3.9 46.9 - - + -
18A PHE* 5.5 1.3 - - + -
33A VAL* 4.3 6.7 - - + -
35A ALA* 1.3 83.6 - - - +
37A VAL* 1.3 61.2 + - - +
38A ASP* 5.0 1.2 - - - +
46A PHE* 4.7 2.9 - - + -
78A LEU* 4.8 3.1 - - + -
85A ILE* 3.7 19.1 - - + -
86A LEU 3.1 10.1 + - - +
87A CYS* 3.6 20.5 - - + +
88A VAL* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE 2.9 4.0 + - - +
8A ASN* 2.9 45.3 - - - +
9A GLY* 2.6 31.6 + - - -
10A PHE 3.4 2.8 + - - -
35A ALA* 4.3 0.4 - - + -
36A VAL* 1.3 72.3 - - - +
38A ASP* 1.3 64.7 + - - +
88A VAL* 3.2 15.0 - - + +
89A LYS 3.8 5.6 - - - +
90A ALA* 3.4 28.7 - - + +
91A GLN 4.6 0.2 - - - +
97A LEU* 3.8 16.2 - - + -
99A TRP* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY* 4.2 4.2 - - - -
10A PHE* 3.2 33.4 + - + +
11A GLY* 3.9 2.6 + - - -
37A VAL* 1.3 83.4 - - - +
39A MET* 1.3 91.5 + - - +
40A ASN* 2.6 24.5 + - - +
46A PHE* 3.7 25.3 - - + -
88A VAL 3.0 5.3 + - - +
89A LYS* 3.3 7.8 - - - -
90A ALA* 2.8 20.3 + - - -
206D VAL* 5.7 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