Contacts of the helix formed by residues 40 - 48 (chain B) in PDB entry 1EQB
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 SER 40 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.6 6.5 - - - -
6A MET* 4.4 10.8 - - - -
39B THR* 1.3 80.5 + - - +
41B PRO* 1.3 74.8 - - - +
42B ARG* 3.1 13.7 + - - +
43B VAL* 3.1 17.2 + - - +
44B MET* 3.4 10.4 + - - +
232B ALA 4.5 1.0 + - - -
278B GLU* 2.9 38.2 + - - -
371B ARG* 3.8 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.3 4.0 - - + +
3A LYS 3.6 18.2 - - - +
4A ARG* 4.0 19.3 - - - +
6A MET* 3.8 34.7 - - + +
39B THR 4.4 1.6 - - - +
40B SER* 1.3 86.9 - - - +
42B ARG* 1.3 55.7 + - - +
43B VAL 3.3 0.2 - - - -
44B MET* 3.4 25.1 + - + +
45B GLN* 2.9 30.3 + - - +
416B TYR* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A MET* 3.0 39.7 - - + +
7A ASN 3.2 31.8 + - - +
8A ILE* 3.7 15.5 - - + +
10A ASP* 4.8 3.8 + - - -
11A TYR* 3.1 62.2 - - - +
40B SER* 3.4 7.2 - - - +
41B PRO* 1.3 77.4 - - - +
43B VAL* 1.3 62.3 + - - +
45B GLN* 3.4 10.0 + - - +
46B ALA* 3.2 17.7 + - - +
274B VAL* 4.0 17.6 - - + +
278B GLU* 2.7 36.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
39B THR* 3.0 32.3 - - + +
40B SER* 3.1 13.3 + - - +
42B ARG* 1.3 75.1 - - - +
44B MET* 1.3 66.2 + - - +
46B ALA* 3.4 3.8 + - - +
47B GLN* 3.1 24.6 + - - +
232B ALA 5.0 0.2 - - - +
233B GLY* 4.7 0.2 - - - -
234B PRO* 3.5 36.6 - - + -
271B GLY* 3.9 10.3 - - - +
274B VAL* 3.8 22.2 - - + -
275B ALA* 3.9 17.0 - - + -
278B GLU* 4.4 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 5.8 3.8 - - - +
48A GLY* 3.5 25.9 - - - +
49A SER 3.7 26.5 - - - +
50A GLN* 4.1 17.0 - - + -
52A THR* 4.2 6.5 - - + -
39B THR* 3.9 12.6 - - + -
40B SER 3.4 6.0 + - - +
41B PRO* 3.5 32.8 - - + +
42B ARG 3.3 0.2 - - - -
43B VAL* 1.3 74.5 - - - +
45B GLN* 1.3 66.2 + - - +
47B GLN* 3.1 10.0 + - - +
48B GLY* 3.0 18.7 + - - -
416B TYR* 3.8 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A MET 4.0 4.2 - - - +
7A ASN* 3.2 32.9 - - - +
8A ILE* 3.7 21.4 - - + +
9A ALA* 4.7 0.4 - - - +
16A TRP* 3.3 33.9 - - + -
19A MET* 4.8 1.8 - - + +
41B PRO 2.9 15.8 + - - +
42B ARG 3.5 6.5 - - - +
43B VAL 3.3 0.2 - - - -
44B MET* 1.3 77.6 - - - +
46B ALA* 1.3 62.5 + - - +
48B GLY* 3.2 11.0 + - - -
49B SER* 3.5 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.1 10.5 - - + +
19A MET* 4.0 11.9 - - + -
42B ARG 3.2 8.5 + - - +
43B VAL 3.5 9.0 - - - +
44B MET 3.2 0.4 - - - -
45B GLN* 1.3 79.7 - - - +
47B GLN* 1.3 57.6 + - - +
49B SER* 2.8 31.0 + - - -
267B HIS* 3.6 7.2 - - - +
270B ALA* 4.0 11.2 - - + +
271B GLY* 3.5 29.8 - - - +
274B VAL* 4.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 3.5 28.1 + - + +
49A SER 5.3 0.2 + - - -
52A THR* 3.4 28.5 + - - +
267A HIS* 3.5 27.6 + - - +
43B VAL* 3.1 16.0 + - + +
44B MET* 3.1 11.0 + - - +
46B ALA* 1.3 79.1 - - + +
48B GLY* 1.3 56.8 + - - +
49B SER 3.3 1.7 + - - +
234B PRO* 3.1 29.5 - - + +
235B ARG 4.2 1.7 + - - +
267B HIS* 3.2 36.8 + - + +
268B VAL* 3.8 20.3 - - + +
271B GLY* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 3.4 42.3 - - - +
48A GLY* 4.0 5.4 - - - -
44B MET 3.0 12.8 + - - -
45B GLN 3.2 6.9 + - - -
46B ALA 3.0 0.6 + - - -
47B GLN* 1.3 76.5 - - - +
49B SER* 1.3 61.6 + - - +
----------------------------------------------------------
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