Contacts of the helix formed by residues 50 - 64 (chain A) in PDB entry 1D66
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 THR 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.3 18.5 + - + +
49A LEU* 1.3 76.0 + - - +
51A ARG* 1.3 62.5 + - - +
52A ALA* 3.5 16.8 - - + +
53A HIS* 2.9 35.2 + - + +
54A LEU 3.0 9.7 + - - -
49B LEU* 3.6 7.9 - - - +
54B LEU* 5.7 0.5 - - - +
11D G 3.3 13.7 + - - -
12D T 2.8 17.6 + - - +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 1.3 67.8 - - - +
52A ALA* 1.3 63.4 + - - +
54A LEU* 3.1 11.3 + - - +
55A THR* 2.9 43.7 + - + +
58A GLU* 4.4 1.6 + - - -
46B ARG* 3.6 27.3 - - - +
47B SER* 2.7 52.3 + - - +
48B PRO* 4.6 0.4 - - - +
49B LEU* 3.4 30.5 - - + +
12D T 2.9 17.0 + - - +
13D C 2.9 45.4 + - - +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 3.5 13.2 - - + +
51A ARG* 1.3 78.4 - - - +
53A HIS* 1.4 58.1 + - - +
55A THR* 3.4 4.8 + - - -
56A GLU* 2.8 32.9 + - - +
12D T 4.6 0.6 + - - -
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Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 4.0 14.6 - - - -
48A PRO* 3.3 37.0 + - + +
50A THR* 2.9 13.3 + - + +
52A ALA* 1.4 76.0 - - - +
54A LEU* 1.3 61.4 + - - +
56A GLU* 4.0 17.9 + - + -
57A VAL* 3.0 32.1 + - + +
54B LEU* 3.5 13.9 - - + +
58B GLU* 3.1 28.0 - - + -
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR 3.0 6.3 + - - -
51A ARG* 3.1 18.3 + - - +
53A HIS* 1.3 79.8 - - - +
55A THR* 1.3 60.1 + - - +
56A GLU 3.1 0.7 + - - -
57A VAL* 3.4 1.3 - - + +
58A GLU* 2.8 43.0 + - - +
47B SER* 3.1 26.5 - - - +
48B PRO 3.5 22.2 - - - +
49B LEU* 3.9 22.7 - - + -
53B HIS* 3.4 21.8 - - + +
54B LEU* 4.2 18.8 - - + +
57B VAL* 4.0 18.8 - - + -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ARG* 2.9 39.2 + - - +
52A ALA* 3.4 4.9 + - - -
54A LEU* 1.3 74.6 - - - +
56A GLU* 1.3 69.1 + - - +
58A GLU* 3.3 22.0 - - + +
59A SER* 2.8 29.4 + - - +
46B ARG* 5.7 3.4 - - - -
47B SER* 5.0 0.4 - - - +
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 2.8 21.3 + - - +
53A HIS* 4.0 16.3 + - + +
55A THR* 1.3 82.6 + - - +
57A VAL* 1.3 71.3 + - - +
59A SER* 2.9 3.4 + - - -
60A ARG* 2.7 75.9 + - - +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A HIS* 3.0 32.3 - - + +
54A LEU* 3.4 5.4 - - + +
56A GLU* 1.3 95.0 - - - +
58A GLU* 1.3 61.3 + - - +
59A SER 3.2 0.4 + - - -
60A ARG* 4.0 3.6 - - + +
61A LEU* 3.5 5.9 + - - +
54B LEU* 4.8 1.1 - - + -
57B VAL* 3.6 21.6 - - + +
58B GLU* 4.2 29.4 - - + +
61B LEU* 3.0 45.4 - - + +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 2.8 46.9 + - + +
55A THR* 3.3 19.0 + - + +
57A VAL* 1.3 72.0 - - - +
59A SER* 1.4 62.3 + - - +
61A LEU* 4.0 3.6 - - - +
62A GLU* 3.3 25.8 + - - +
47B SER* 2.9 38.9 + - - -
53B HIS* 3.6 6.2 + - + +
57B VAL* 4.0 25.1 - - + +
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 2.8 25.2 + - - +
56A GLU* 2.9 3.0 + - - -
58A GLU* 1.4 81.5 - - - +
60A ARG* 1.3 60.4 + - - -
61A LEU 3.3 0.7 - - - -
62A GLU* 2.8 23.6 - - - +
63A ARG* 3.1 22.6 - - - +
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 2.7 52.8 + - - +
57A VAL* 4.2 3.0 - - - +
59A SER* 1.3 71.9 - - - +
61A LEU* 1.3 64.9 + - - +
63A ARG* 3.4 15.0 - - - +
64A LEU* 3.8 16.2 + - + +
61B LEU* 3.7 29.5 - - + +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A VAL 3.5 4.9 - - - +
58A GLU 4.0 3.8 - - - +
60A ARG* 1.3 78.0 - - - +
62A GLU* 1.3 60.9 + - + +
63A ARG 3.0 3.6 + - - -
64A LEU* 3.0 27.8 + - - +
57B VAL* 3.6 45.5 - - + +
60B ARG* 3.3 39.9 - - + +
61B LEU* 3.4 24.2 - - + +
64B LEU* 3.5 20.5 - - + +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU 3.3 15.2 + - - +
59A SER* 2.8 21.4 - - - +
61A LEU* 1.3 76.1 - - + +
63A ARG* 1.3 75.4 + - - +
64A LEU 5.2 3.3 - - - +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 3.1 27.1 - - - +
60A ARG* 3.4 9.9 - - - +
61A LEU 3.0 0.2 + - - -
62A GLU* 1.3 90.2 + - - +
64A LEU* 1.3 72.1 - - + +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ARG* 4.0 17.7 - - + +
61A LEU* 3.0 20.1 + - - +
62A GLU* 5.0 3.5 - - - +
63A ARG* 1.3 93.9 - - + +
64B LEU* 3.6 26.1 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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