Contacts of the helix formed by residues 48 - 62 (chain A) in PDB entry 4IM0
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 PRO 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ARG* 1.3 88.0 + - - +
49A VAL* 1.3 68.0 + - + +
50A ASP 3.5 2.0 + - - +
51A VAL* 3.6 40.9 + - + +
52A GLN* 4.2 5.2 + - - +
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Residues in contact with VAL 49 (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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47A ARG* 4.1 1.7 - - - +
48A PRO* 1.3 75.7 - - + +
50A ASP* 1.3 75.5 - - + +
51A VAL 3.6 0.2 + - - -
52A GLN* 3.6 11.8 + - - +
53A MET* 3.7 8.1 + - + +
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Residues in contact with ASP 50 (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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48A PRO* 4.7 1.2 - - - +
49A VAL* 1.3 91.0 - - + +
51A VAL* 1.3 63.9 + - - +
52A GLN 3.0 2.2 - - - -
53A MET* 3.2 21.8 - - - +
54A ARG* 3.1 46.6 + - + +
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Residues in contact with VAL 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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47A ARG 5.3 0.2 - - - -
48A PRO* 3.6 45.1 - - + +
49A VAL 3.4 0.6 - - - -
50A ASP* 1.3 78.5 - - - +
52A GLN* 1.3 59.0 + - - +
54A ARG* 3.4 26.7 + - - +
55A GLU* 3.2 37.9 + - - +
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Residues in contact with GLN 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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20A THR* 5.0 4.2 - - - +
40A PHE* 3.6 34.9 - - - +
48A PRO 4.2 4.2 + - - +
49A VAL 3.6 8.8 + - - +
50A ASP 3.0 0.4 - - - -
51A VAL* 1.3 78.0 - - - +
53A MET* 1.3 55.2 + - - +
54A ARG 3.1 1.8 - - - -
55A GLU* 3.2 11.0 + - + +
56A PHE* 2.7 73.8 + - + -
82A LYS* 5.6 1.9 - - - +
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Residues in contact with MET 53 (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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49A VAL* 3.7 4.7 + - + +
50A ASP* 3.2 31.8 + - - +
52A GLN* 1.3 78.4 - - - +
54A ARG* 1.3 61.2 + - + +
56A PHE* 3.7 13.7 - - - +
57A GLU* 3.3 19.8 + - - +
73A ILE* 5.3 5.6 - - + +
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Residues in contact with ARG 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 ASP* 3.1 40.0 + - + +
51A VAL* 3.4 37.2 + - - +
52A GLN 3.1 0.6 - - - -
53A MET* 1.3 76.5 - - + +
55A GLU* 1.3 60.8 + - + +
57A GLU* 2.9 23.2 + - - +
58A VAL* 3.0 17.1 + - + +
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Residues in contact with GLU 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 VAL* 3.2 32.4 + - - +
52A GLN* 3.2 13.1 + - + +
54A ARG* 1.3 79.0 - - + +
56A PHE* 1.3 63.3 + - + +
58A VAL* 3.6 12.3 + - + +
59A LEU* 3.1 35.3 + - + +
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Residues in contact with PHE 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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40A PHE* 3.8 23.1 - + - -
52A GLN* 2.7 67.7 + - + +
53A MET* 3.7 8.5 - - - +
54A ARG 3.1 0.2 - - - -
55A GLU* 1.3 76.5 - - + +
57A GLU* 1.3 61.1 + - - +
59A LEU* 3.4 5.4 + - + -
60A LYS* 3.2 18.0 + - - +
70A LEU* 3.3 14.4 - - + +
73A ILE* 3.4 36.3 - - + -
82A LYS* 4.4 13.0 - - + -
84A LEU* 3.4 37.7 - - + -
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Residues in contact with GLU 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 MET 3.3 11.2 + - - +
54A ARG* 2.9 13.3 + - - +
56A PHE* 1.3 77.8 - - - +
58A VAL* 1.3 64.4 + - + +
60A LYS* 3.1 33.8 + - - +
61A LYS* 3.3 37.6 + - + +
73A ILE* 6.0 1.7 - - - +
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Residues in contact with VAL 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 ARG* 3.0 19.2 + - + +
55A GLU* 3.6 15.5 - - + -
57A GLU* 1.3 74.8 - - + +
59A LEU* 1.3 79.7 + - + +
61A LYS* 3.3 17.3 + - - +
62A LEU* 3.5 18.1 + - + +
131A ILE* 5.0 18.4 - - + -
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Residues in contact with LEU 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 GLU* 3.1 24.7 - - + +
56A PHE* 3.4 9.7 + - + +
57A GLU 3.2 0.8 - - - -
58A VAL* 1.3 91.0 - - + +
60A LYS* 1.3 64.2 + - - +
61A LYS 3.1 0.7 - - - -
62A LEU* 3.3 26.7 + - + +
70A LEU* 3.6 31.8 + - + +
84A LEU* 5.7 5.8 - - + -
86A MET* 5.8 5.4 - - + -
131A ILE* 5.9 4.3 - - + -
158A PHE* 4.4 37.7 - - + +
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PHE 3.2 12.4 + - - +
57A GLU* 3.1 30.8 + - - +
59A LEU* 1.3 77.0 - - - +
61A LYS* 1.3 62.6 + - + +
62A LEU 4.3 3.5 - - - +
69A LYS* 6.1 0.3 - - - +
70A LEU* 3.6 22.3 - - + +
71A PHE 3.2 29.3 + - - +
72A ALA* 4.3 13.3 - - - +
73A ILE* 4.7 14.0 - - + +
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Residues in contact with LYS 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 GLU* 3.3 38.0 + - + +
58A VAL* 3.5 11.0 - - - +
59A LEU 3.1 0.8 - - - -
60A LYS* 1.3 78.9 - - + +
62A LEU* 1.3 66.3 + - + +
63A ASN* 3.1 9.7 + - - +
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Residues in contact with LEU 62 (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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58A VAL* 3.5 15.7 + - + +
59A LEU* 3.3 23.2 + - + +
60A LYS 4.3 3.6 - - - +
61A LYS* 1.3 76.8 - - + +
63A ASN* 1.3 58.9 + - - +
64A HIS 4.0 1.4 + - - -
67A ILE* 4.3 23.8 - - + +
69A LYS* 5.1 13.7 - - - +
70A LEU 5.5 0.7 + - - -
125A HIS* 4.0 16.4 - - + +
126A LEU* 4.1 26.0 - - + -
129A ASN* 4.1 28.0 - - + +
131A ILE* 4.6 13.5 - - + -
158A PHE* 4.3 11.4 - - + -
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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