Contacts of the helix formed by residues 52 - 65 (chain A) in PDB entry 3D7S
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 52 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.1 25.6 - - - -
50A GLU 3.4 2.3 + - - -
51A ALA* 1.3 79.3 - - - +
53A THR* 1.3 68.1 + - - +
54A ARG* 2.5 42.9 + - - +
55A THR* 3.1 17.9 + - - -
56A ARG* 3.2 3.5 + - - +
74A SER* 3.7 3.2 + - - -
105A ARG* 3.0 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER* 1.3 71.6 - - - +
54A ARG* 1.3 60.6 + - - +
56A ARG* 2.6 56.3 + - - +
57A LEU* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA 5.3 0.2 + - - -
52A SER* 2.5 38.1 + - - +
53A THR* 1.3 78.9 - - - +
55A THR* 1.3 74.2 + - + +
57A LEU* 3.3 6.6 + - - +
58A SER* 3.1 22.3 + - - -
105A ARG* 3.3 19.2 - - - +
167A ARG* 5.4 7.1 - - - +
267A LEU 4.7 5.1 + - - -
268A PRO* 3.6 33.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.1 25.8 - - - -
52A SER* 3.1 17.0 + - - +
54A ARG* 1.3 94.2 - - + +
56A ARG* 1.3 58.3 + - - +
58A SER* 4.0 6.5 - - - -
59A PHE* 3.0 35.3 + - - +
105A ARG* 4.4 9.3 + - - +
127A ALA* 5.4 3.4 - - - -
134A HIS* 4.3 24.5 - - + +
137A GLN* 5.9 0.7 - - - +
167A ARG* 6.0 0.7 - - - +
296A ARG* 4.8 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 3.9 2.0 - - - +
48A PHE* 3.5 33.0 - - + -
52A SER 3.2 10.0 + - - +
53A THR* 2.6 63.0 + - - +
55A THR* 1.3 73.4 + - - +
57A LEU* 1.3 62.8 + - - +
59A PHE* 3.4 1.0 + - - +
60A GLU* 2.7 72.8 + - - +
73A PHE 5.4 3.1 - - - +
74A SER* 3.3 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A THR* 2.9 34.4 + - + +
54A ARG* 4.0 6.1 - - - +
56A ARG* 1.3 85.0 - - - +
58A SER* 1.3 58.1 + - - +
60A GLU* 4.5 10.1 - - + +
61A THR* 2.6 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG 3.1 15.0 + - - -
55A THR* 4.0 2.2 - - - -
57A LEU* 1.3 76.5 - - - +
59A PHE* 1.3 59.3 + - - +
62A SER* 2.9 27.8 + - - -
289A ALA 4.6 6.2 + - - -
292A GLY 4.1 6.8 + - - -
293A ILE* 3.0 30.0 - - - +
296A ARG* 2.8 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 5.8 0.4 - - - +
48A PHE* 5.5 3.1 - + + -
55A THR* 3.0 18.5 + - - +
56A ARG* 3.7 3.6 - - - +
58A SER* 1.3 80.0 - - - +
60A GLU* 1.3 62.6 + - + +
62A SER* 2.9 27.8 + - - -
63A MET* 3.1 23.2 - - + +
103A VAL* 3.7 38.8 - - + -
125A LEU* 4.4 15.0 - - + -
126A ASN 5.1 1.6 - - - -
127A ALA* 4.3 20.0 - - + -
134A HIS* 6.4 0.2 - + - -
136A THR* 3.7 25.6 - - + -
296A ARG* 3.7 37.4 - - + +
299A LEU* 5.9 1.3 - - + -
300A LEU* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 2.9 24.9 + - - +
56A ARG* 2.7 57.2 + - - +
57A LEU* 4.0 9.4 - - + +
59A PHE* 1.3 69.5 - - - +
61A THR* 1.3 66.9 + - - +
63A MET* 2.8 26.0 + - - +
64A HIS* 2.9 21.0 + - + +
70A VAL* 3.9 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 2.6 34.0 + - - +
58A SER* 3.7 3.3 - - - -
60A GLU* 1.3 67.6 - - - +
62A SER* 1.3 54.5 + - - +
63A MET 2.4 18.3 + - - -
64A HIS* 2.9 17.3 + - + +
65A ARG* 3.2 42.2 + - + +
293A ILE* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A SER 2.9 16.2 + - - -
59A PHE* 2.9 12.6 + - - -
61A THR* 1.3 74.2 - - - +
63A MET* 1.3 53.7 + - - +
65A ARG* 4.9 1.6 - - - -
66A LEU* 5.1 1.2 - - - +
293A ILE* 3.0 43.7 - - - +
296A ARG* 3.1 23.5 - - - +
297A GLN* 3.5 15.0 + - - +
300A LEU* 2.9 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 4.1 22.0 - - + -
46A SER* 4.0 17.7 - - - -
59A PHE* 3.1 35.4 - - + +
60A GLU* 2.8 22.4 - - - +
61A THR 2.4 13.7 + - - -
62A SER* 1.3 69.6 - - - +
64A HIS* 1.3 62.1 + - - +
65A ARG 3.3 0.7 - - - -
66A LEU* 3.4 10.1 + - - +
68A ALA* 3.4 29.3 - - + +
70A VAL* 3.8 29.6 - - + -
103A VAL* 4.0 28.0 - - + -
300A LEU* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 2.9 29.5 + - + -
61A THR* 2.9 8.1 + - - +
63A MET* 1.3 74.1 - - - +
65A ARG* 1.3 53.2 + - + +
66A LEU 2.6 18.1 + - - -
67A GLY* 2.6 18.1 + - - -
68A ALA 3.7 14.8 - - - -
69A SER* 5.2 0.9 - - - -
70A VAL* 3.2 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 6.1 0.9 - - - +
35A GLN 4.1 1.0 + - - -
36A PRO* 3.4 23.5 - - - +
61A THR* 3.2 35.6 + - + +
62A SER* 4.9 0.9 - - - -
63A MET 3.3 0.2 - - - -
64A HIS* 1.3 75.3 - - + +
66A LEU* 1.3 64.0 + - + +
67A GLY 3.6 0.7 - - - -
293A ILE* 4.7 10.5 - - + +
297A GLN* 3.3 23.0 - - - +
----------------------------------------------------------
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