Contacts of the strand formed by residues 3 - 8 (chain B) 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 3 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 4.2 9.9 - - - +
2B PRO* 1.3 71.6 - - - +
4B LYS* 1.3 59.7 + - - +
5B VAL* 3.2 19.7 + - + +
30B GLU 3.4 17.3 + - - +
31B ILE* 3.5 16.1 - - + +
32B ASP* 2.9 25.8 + - - +
105B GLU* 4.0 9.6 - - - +
106B TYR* 3.6 29.4 - - + -
347B VAL* 4.7 4.0 - - + -
348B ARG* 6.1 1.3 - - - -
351B ALA* 3.7 28.0 - - + +
355B ARG* 5.6 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PRO 3.4 7.8 + - - +
3B ILE* 1.3 70.5 - - - +
5B VAL* 1.3 61.6 + - - +
32B ASP* 3.6 18.4 - - - +
34B VAL* 3.9 12.1 - - + -
102B LEU 3.9 15.1 + - - +
103B GLY* 2.8 35.9 - - - +
104B VAL* 4.4 0.4 - - - -
105B GLU* 3.2 32.2 + - + +
106B TYR* 3.4 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 3.6 20.9 - - + +
4B LYS* 1.3 76.6 - - - +
6B GLY* 1.3 79.8 + - - +
7B ILE* 4.8 4.5 - - + -
21B LEU* 5.6 4.3 - - + -
31B ILE* 3.4 34.3 - - + -
32B ASP 3.1 11.0 + - - +
33B VAL* 3.5 8.4 - - + -
34B VAL* 2.8 31.0 + - - +
104B VAL* 3.7 4.0 - - - -
106B TYR* 3.1 17.9 - - + +
108B ILE* 3.8 21.5 - - + -
347B VAL* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 1.3 77.2 - - - +
7B ILE* 1.3 58.2 + - - -
8B ASN 4.0 1.1 - - - -
33B VAL* 4.8 0.4 - - - -
35B ALA 3.5 10.3 - - - -
99B TRP* 4.2 9.2 - - - -
104B VAL* 3.4 15.6 - - - +
106B TYR 2.9 6.3 + - - -
107B VAL* 3.2 4.5 - - - -
108B ILE* 2.6 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.8 2.7 - - + -
6B GLY* 1.3 78.3 - - - +
8B ASN* 1.3 60.8 + - - +
9B GLY 3.4 18.2 + - - +
10B PHE* 4.1 11.2 - - + -
14B GLY* 4.1 24.0 - - - +
17B VAL* 5.0 6.7 - - + -
18B PHE* 4.2 21.3 - - + +
21B LEU* 5.6 3.1 - - + -
33B VAL* 3.8 26.5 - - + -
35B ALA 3.1 7.7 + - - -
36B VAL* 3.4 16.3 - - + +
37B VAL* 3.2 22.2 + - - +
99B TRP* 4.5 0.8 - - - -
108B ILE* 3.8 24.0 - - + +
110B SER* 4.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLY 4.0 2.2 + - - -
7B ILE* 1.3 71.6 - - - +
9B GLY* 1.3 74.2 + - - +
37B VAL* 3.2 31.4 + - + +
90B ALA* 5.6 0.6 - - - +
91B GLN 6.0 0.2 - - - +
97B LEU* 5.3 4.1 - - - +
99B TRP* 4.1 0.7 - - + -
107B VAL* 4.0 8.4 - - + +
108B ILE 3.0 9.7 + - - +
109B GLU* 3.0 23.8 - - - +
110B SER* 3.2 23.4 + - - -
111B THR* 3.2 17.6 - - - +
114B PHE* 3.5 11.0 - - - -
123B HIS* 3.2 26.1 + - + -
1362B NAD 4.6 4.9 + - - -
----------------------------------------------------------
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