Contacts of the helix formed by residues 56 - 69 (chain A) in PDB entry 1HUM
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 GLU 56 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP* 3.0 24.0 + - + +
54A PRO 4.1 2.7 - - - +
55A SER* 1.3 78.0 - - - +
57A SER* 1.3 67.4 + - - +
58A TRP* 2.7 44.3 + - + +
59A VAL* 2.8 23.0 + - + +
60A GLN 3.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER 3.3 5.8 + - - -
56A GLU* 1.3 71.1 - - - +
58A TRP* 1.3 63.9 + - - +
60A GLN* 3.0 15.1 + - - +
61A GLU* 2.9 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 5.4 7.2 - - + -
18A ARG 4.9 2.2 - - - -
19A LYS* 3.5 61.8 - - + +
20A LEU* 4.4 12.3 - - + -
42A PHE* 3.1 45.3 - + - -
52A ALA* 4.1 7.4 - - + -
56A GLU* 2.7 39.0 + - + +
57A SER* 1.3 82.4 + - - +
59A VAL* 1.3 73.7 + - + +
61A GLU* 4.1 10.1 - - - -
62A TYR* 2.8 54.1 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 4.1 19.1 - - + -
42A PHE* 3.8 19.2 - - + -
52A ALA* 3.9 12.1 - - + -
53A ASP 3.3 25.4 - - - +
54A PRO* 4.2 9.0 - - + -
56A GLU* 2.8 15.8 + - + +
58A TRP* 1.3 119.1 - - + +
60A GLN* 1.3 62.6 + - - +
62A TYR 3.4 0.2 + - - -
63A VAL* 3.1 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PRO* 4.3 15.0 + - - +
56A GLU 3.5 2.1 + - - +
57A SER* 3.0 15.8 + - - +
59A VAL* 1.3 80.7 - - - +
61A GLU* 1.3 63.4 + - - +
63A VAL* 3.3 9.2 + - + +
64A TYR* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 2.9 14.5 + - - +
58A TRP* 3.6 13.0 - - - +
60A GLN* 1.3 78.6 - - - +
62A TYR* 1.3 72.0 + - + +
64A TYR* 3.1 9.1 + - + +
65A ASP* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 3.0 34.3 - - + +
20A LEU 3.1 21.9 + - - -
21A PRO* 4.3 2.3 - - - +
22A ARG* 3.7 36.7 + - + +
25A VAL* 4.6 14.8 - - + -
42A PHE* 3.8 20.9 - + + -
58A TRP* 2.8 45.6 + + + +
61A GLU* 1.3 84.7 - - + +
63A VAL* 1.3 63.2 + - - +
65A ASP* 3.3 11.8 + - - +
66A LEU* 3.0 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.5 19.7 - - + +
30A GLU* 5.5 3.6 - - - +
40A VAL* 3.9 35.9 - - + -
42A PHE* 4.1 6.5 - - + -
59A VAL 3.1 17.4 + - - +
60A GLN* 3.5 11.4 - - + +
61A GLU 3.2 0.2 - - - -
62A TYR* 1.3 76.5 - - - +
64A TYR* 1.3 63.7 + - - +
66A LEU* 3.0 10.7 + - - +
67A GLU* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN 3.0 13.2 + - - +
61A GLU* 3.4 13.2 - - + +
63A VAL* 1.3 79.2 - - - +
65A ASP* 1.3 65.1 + - - +
67A GLU* 3.0 26.7 + - + +
68A LEU* 3.1 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 4.0 34.1 + - - +
61A GLU* 3.0 31.7 + - - +
62A TYR* 3.6 15.5 - - - +
63A VAL 3.2 0.2 - - - -
64A TYR* 1.3 79.7 - - - +
66A LEU* 1.3 63.1 + - + +
68A LEU* 3.3 15.1 + - - +
69A ASN* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 5.7 5.6 - - - +
25A VAL* 4.3 16.6 - - + +
26A VAL 4.1 8.5 - - - +
27A ASP* 3.9 26.2 - - - +
28A TYR* 3.6 45.2 - - + -
42A PHE* 4.1 14.8 - - + -
62A TYR* 3.0 20.0 + - + +
63A VAL* 3.0 9.1 + - - +
65A ASP* 1.3 78.9 - - + +
67A GLU* 1.3 61.6 + - - +
69A ASN* 3.2 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.5 13.0 + - - +
63A VAL* 3.0 35.5 + - + +
64A TYR* 3.0 19.8 + - + +
66A LEU* 1.3 79.9 - - - +
68A LEU* 1.3 66.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.1 49.5 + - + +
65A ASP* 3.8 15.9 - - - +
66A LEU 3.3 0.4 - - - -
67A GLU* 1.3 83.6 - - + +
69A ASN* 1.3 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 4.9 12.9 + - - +
65A ASP 3.2 16.2 + - - +
66A LEU* 3.2 19.4 - - - +
68A LEU* 1.3 81.4 - - + +
----------------------------------------------------------
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