Contacts of the strand formed by residues 37 - 43 (chain B) in PDB entry 1A4I
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 ARG 37 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR 3.8 4.3 - - - +
36B PRO* 1.3 75.4 - - - +
38B LEU* 1.3 69.6 - - - +
65B ILE* 4.4 1.8 - - - +
66B LYS* 3.1 46.0 - - + +
68B THR* 2.8 41.5 + - - +
91B ASP* 4.0 6.5 + - - -
93B THR* 2.8 48.6 + - - +
94B VAL* 3.7 19.6 - - + +
95B HIS* 2.9 35.1 + - - +
96B GLY 3.3 8.0 + - - +
287B THR* 4.5 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 1.3 79.9 - - - +
39B ALA* 1.3 73.9 + - - +
40B ILE* 4.4 16.6 - - + -
56B LYS 5.3 0.7 - - - +
60B ALA* 4.6 2.0 - - + -
65B ILE* 4.0 14.2 - - + +
66B LYS 2.8 6.9 + - - +
67B ALA* 3.2 14.2 - - + +
68B THR* 2.8 25.8 + - - -
94B VAL* 4.8 0.2 - - - -
96B GLY 3.3 15.3 - - - +
97B PHE* 4.2 0.4 - - - -
98B LEU* 4.4 5.8 - - + -
124B VAL* 3.9 19.3 - - + -
283B LEU* 4.5 7.4 - - + -
284B MET* 4.1 28.5 - - + -
287B THR* 3.7 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 5.9 0.2 - - - +
38B LEU* 1.3 76.1 - - - +
40B ILE* 1.3 67.4 + - - +
68B THR* 3.3 20.0 - - + +
70B ILE* 5.1 2.7 - - + -
88B LEU* 3.8 31.6 - - + -
94B VAL* 4.2 8.2 - - + +
96B GLY 3.0 8.9 + - - -
97B PHE* 3.1 12.9 - - + +
98B LEU 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.4 14.1 - - + -
39B ALA* 1.3 79.7 - - - +
41B LEU* 1.3 65.3 - - - +
53B ILE* 3.9 37.2 - - + -
56B LYS* 3.9 36.6 - - + -
57B LEU* 4.0 20.0 - - + -
68B THR 2.8 12.9 + - - +
69B HIS* 3.5 7.3 - - + -
70B ILE* 2.9 27.3 + - - +
98B LEU* 3.5 31.0 - - + -
100B GLN* 4.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 4.2 0.6 - - - +
40B ILE* 1.3 73.6 - - - +
42B GLN* 1.3 61.8 + - - +
43B VAL* 5.1 1.6 - - + -
70B ILE* 3.5 36.6 - - + +
72B LEU* 3.9 20.0 - - + -
81B VAL* 4.2 16.6 - - + -
84B TYR* 4.1 19.7 - - + -
85B ILE* 4.0 28.0 - - + +
88B LEU* 4.6 15.0 - - + -
97B PHE* 5.4 0.4 - - + -
98B LEU 2.9 13.6 + - - +
99B VAL* 3.5 16.2 - - + +
100B GLN 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 1.3 74.8 - - - +
43B VAL* 1.3 71.7 + - - +
44B GLY 3.7 22.3 + - - +
45B ASN* 4.0 6.3 - - - +
46B ARG 4.1 1.6 - - - +
49B SER* 3.7 20.6 - - - -
50B ASN* 2.8 23.7 + - - +
53B ILE* 3.4 18.0 - - + +
69B HIS* 2.7 43.9 + - - +
70B ILE 2.9 7.4 + - - +
71B LYS* 3.3 11.6 - - + -
72B LEU* 2.8 31.5 + - - +
100B GLN* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.4 4.5 + - + -
42B GLN* 1.3 82.5 + - - +
44B GLY* 1.3 65.2 + - - +
46B ARG 5.4 0.2 + - - -
72B LEU* 3.7 11.2 - - + -
73B PRO 4.0 11.9 - - - +
76B THR* 4.2 9.4 - - - -
81B VAL* 3.6 30.3 - - + -
99B VAL* 5.7 0.4 - - + -
100B GLN 5.1 2.0 + - - -
102B PRO 4.8 1.6 - - - +
103B LEU* 3.9 30.2 - - + +
104B ASP* 3.0 38.6 + - - +
105B SER* 4.0 17.7 - - - -
109B ILE* 4.7 4.7 - - + -
----------------------------------------------------------
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