Contacts of the helix formed by residues 30 - 42 (chain B) in PDB entry 1VEW
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 HIS 30 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU* 3.8 10.5 - - - -
174A TYR* 2.6 31.6 + + - -
179A ASN* 3.6 27.8 - - + +
25B ILE* 3.2 16.7 + - + -
26B HIS* 3.3 25.8 - - + +
29B LYS* 1.3 76.4 - - - +
31B HIS* 1.3 63.6 + - - +
33B THR* 3.3 9.0 + - - -
34B TYR* 3.2 39.5 + - + -
171B HIS* 3.5 34.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.5 13.9 - - + +
5B PRO* 3.7 19.1 - - + -
26B HIS 3.0 12.8 + - - +
27B HIS* 3.3 16.5 + - - +
29B LYS 3.5 0.2 - - - -
30B HIS* 1.3 74.2 - - - +
32B GLN* 1.3 63.3 + - - +
34B TYR* 3.1 9.8 + - + +
35B VAL* 3.0 21.5 + - + +
77B GLY 4.4 1.1 - - - -
78B HIS* 3.1 41.3 + - - -
81B HIS* 3.7 23.2 - - + +
82B SER* 3.6 17.5 - - - -
85B TRP* 3.0 29.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.7 28.6 - - + +
27B HIS 3.4 5.1 + - - +
28B THR 3.2 27.2 - - - +
29B LYS* 3.7 3.8 - - - +
30B HIS 3.3 0.4 - - - -
31B HIS* 1.3 77.6 - - - +
33B THR* 1.3 57.0 + - - +
35B VAL* 3.3 13.2 + - - +
36B ASN* 2.8 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASN* 5.7 2.6 + - - -
29B LYS 3.0 18.9 + - - -
30B HIS* 3.5 7.2 - - - +
32B GLN* 1.3 74.0 - - - +
34B TYR* 1.3 66.6 + - + +
36B ASN* 3.3 9.0 + - + +
37B ASN* 2.9 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 3.8 25.3 - + - -
30B HIS* 3.2 32.4 + - + -
31B HIS* 3.1 9.2 + - - +
33B THR* 1.3 82.4 - - + +
35B VAL* 1.3 57.0 - - - +
38B ALA* 3.0 31.6 + - - +
73B ASN 4.3 7.6 - - - -
74B ASN* 3.4 35.5 - - - +
77B GLY* 4.0 12.1 - - - -
78B HIS* 4.0 8.7 - - - +
81B HIS* 3.5 28.9 - + - -
146B GLN* 3.0 21.9 + - + -
169B TRP* 3.8 18.2 - - - -
171B HIS* 4.1 7.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B TYR* 3.7 17.0 - - + +
3B THR* 4.8 0.2 - - - -
4B LEU* 4.3 21.5 - - + +
31B HIS* 3.0 22.3 + - + +
32B GLN* 3.5 19.5 - - - +
34B TYR* 1.3 75.1 - - - +
36B ASN* 1.3 59.6 + - - +
38B ALA* 3.4 4.0 + - - +
39B ASN* 3.0 48.2 + - - +
78B HIS* 3.5 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 2.8 52.5 + - - +
33B THR* 3.3 9.0 + - - +
35B VAL* 1.3 76.2 - - - +
37B ASN* 1.3 61.4 + - - +
39B ASN* 3.4 8.3 + - - +
40B ALA* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 2.9 34.9 + - - +
36B ASN* 1.3 77.2 - - - +
38B ALA* 1.3 64.8 + - - +
40B ALA* 3.5 8.4 + - - +
41B ALA* 3.2 22.2 + - - +
70B VAL* 4.6 7.2 - - + +
74B ASN* 3.4 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B TYR* 4.1 24.0 - - + -
34B TYR 3.0 20.2 + - - +
35B VAL* 3.8 4.0 - - - +
37B ASN* 1.3 76.7 - - - +
39B ASN* 1.3 59.4 + - - +
41B ALA* 3.3 3.1 + - - +
42B LEU* 2.9 35.1 + - - +
70B VAL 5.6 0.2 - - - -
71B LEU* 4.2 10.8 - - + -
74B ASN* 3.8 13.4 - - + +
75B ALA* 4.2 11.2 - - - +
78B HIS* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER* 3.5 15.6 - - - -
2B TYR* 2.8 54.6 + - - +
35B VAL* 3.0 29.0 + - - +
36B ASN* 3.7 7.4 + - - +
38B ALA* 1.3 73.4 - - - +
40B ALA* 1.3 63.9 + - - +
42B LEU* 3.2 7.7 + - - +
43B GLU* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASN 3.0 16.2 + - - +
37B ASN* 3.7 11.2 - - - +
38B ALA 3.3 0.2 - - - -
39B ASN* 1.3 76.4 - - - +
41B ALA* 1.3 61.5 - - - +
43B GLU* 3.5 21.7 - - - +
44B SER 5.0 0.3 + - - -
67B LYS* 4.8 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN 3.2 14.5 + - - +
38B ALA 3.3 5.3 + - - +
40B ALA* 1.3 79.1 - - - +
42B LEU* 1.3 63.1 + - - +
43B GLU 3.3 0.8 + - - -
44B SER* 4.1 4.2 + - - -
45B LEU* 4.6 5.7 - - - +
67B LYS* 3.5 32.9 + - + +
70B VAL* 4.1 24.7 - - + -
71B LEU* 4.0 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER* 6.2 3.1 - - - -
2B TYR* 3.6 42.4 - - + +
38B ALA 2.9 18.2 + - - +
39B ASN* 3.2 9.1 + - - +
41B ALA* 1.3 75.8 - - - +
43B GLU* 1.3 58.4 + - - +
44B SER 3.3 2.5 - - - -
45B LEU* 3.0 32.9 + - + +
48B PHE* 4.1 25.8 - - + +
49B ALA* 3.8 26.2 - - + +
56B LEU* 4.3 8.3 - - + -
71B LEU* 3.9 26.9 - - + -
----------------------------------------------------------
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