Contacts of the helix formed by residues 58 - 71 (chain A) in PDB entry 1REU
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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASN* 5.7 0.2 - - - +
57A SER* 1.3 76.3 + - - +
59A ASN* 1.3 66.8 + - - +
60A HIS* 4.0 7.2 + - - +
61A ALA* 2.9 30.0 + - - +
62A ILE* 3.0 15.1 + - - +
113A CYS 3.8 3.2 + - - -
114A ARG* 3.3 41.9 + - - +
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Residues in contact with ASN 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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2A MPD 3.3 56.2 + - + +
57A SER 4.1 1.4 + - - -
58A THR* 1.3 71.2 - - - +
60A HIS* 1.3 63.3 + - - +
62A ILE* 3.0 12.5 + - - +
63A VAL* 2.9 28.3 + - + +
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Residues in contact with HIS 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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58A THR* 3.2 7.7 + - - +
59A ASN* 1.3 79.6 - - - +
61A ALA* 1.3 59.0 + - - +
63A VAL* 3.3 12.5 + - + +
64A GLN* 2.9 50.8 + - + +
114A ARG 4.7 9.6 - - - +
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Residues in contact with ALA 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 SER* 3.7 13.7 - - - +
58A THR* 2.9 23.3 + - - +
60A HIS* 1.3 76.4 - - - +
62A ILE* 1.3 64.5 + - - +
64A GLN* 4.5 3.1 - - - -
65A THR* 3.0 29.5 + - - -
77A ALA* 3.7 22.1 - - + +
113A CYS* 3.8 13.9 - - + +
114A ARG 3.9 10.8 - - - -
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Residues in contact with ILE 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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2A MPD 4.1 27.4 - - - +
51A PRO* 3.9 30.5 - - + -
57A SER* 3.6 21.8 - - - +
58A THR 3.0 15.3 + - - +
59A ASN* 3.4 15.0 - - - +
61A ALA* 1.3 77.3 - - - +
63A VAL* 1.3 65.0 + - + +
65A THR* 3.3 7.6 + - - -
66A LEU* 3.1 31.8 + - + +
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Residues in contact with VAL 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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2A MPD 5.3 11.4 - - + -
59A ASN* 2.9 19.8 + - + +
60A HIS* 3.3 15.2 + - + +
62A ILE* 1.3 81.7 - - + +
64A GLN* 1.3 56.5 + - - +
66A LEU* 3.3 9.7 + - + +
67A VAL* 3.0 37.3 + - + +
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Residues in contact with GLN 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 HIS* 2.9 41.0 + - + +
61A ALA* 3.9 6.2 - - - +
63A VAL* 1.3 75.4 - - - +
65A THR* 1.3 61.7 + - - +
67A VAL* 3.5 6.2 + - - +
68A ASN* 3.0 28.1 + - - +
74A ILE* 3.9 13.4 - - + +
75A PRO* 2.6 39.7 + - - +
76A LYS 3.3 13.9 + - - -
77A ALA* 4.5 7.0 - - - +
114A ARG* 5.3 3.6 - - - +
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Residues in contact with THR 65 (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 CYS* 4.4 7.1 + - - +
48A PRO 3.3 27.1 + - - +
49A PHE* 3.5 22.3 - - + -
51A PRO* 4.7 7.2 - - + -
61A ALA 3.0 20.4 + - - -
62A ILE* 3.5 8.3 - - - +
64A GLN* 1.3 77.3 - - - +
66A LEU* 1.3 62.0 + - - +
68A ASN* 3.4 9.5 - - - +
69A SER* 3.3 18.0 + - - -
76A LYS* 4.1 9.4 - - + +
77A ALA* 3.6 19.7 + - - +
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Residues in contact with LEU 66 (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 PHE* 3.4 33.4 - - + -
51A PRO* 4.4 14.1 - - + -
62A ILE* 3.1 23.6 + - + +
63A VAL* 3.6 12.3 - - + +
64A GLN 3.2 0.2 - - - -
65A THR* 1.3 74.7 - - - +
67A VAL* 1.3 65.5 + - + +
68A ASN 3.0 1.1 - - - -
69A SER* 2.7 25.8 + - - +
70A VAL* 3.6 7.1 + - - +
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Residues in contact with VAL 67 (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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63A VAL* 3.0 31.7 + - + +
64A GLN* 3.5 7.6 + - - +
66A LEU* 1.3 77.2 - - + +
68A ASN* 1.3 58.1 + - - +
70A VAL* 3.1 11.3 - - + +
71A ASN* 2.8 35.7 + - + +
74A ILE* 4.1 28.3 - - + -
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Residues in contact with ASN 68 (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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64A GLN 3.0 17.3 + - - +
65A THR* 3.4 8.2 - - - +
66A LEU 3.0 0.4 - - - -
67A VAL* 1.3 75.5 - - - +
69A SER* 1.3 67.2 + - - +
71A ASN 2.6 24.4 + - - +
72A SER* 3.9 14.5 + - - +
74A ILE 2.4 34.6 + - - +
75A PRO* 3.6 1.2 - - - +
76A LYS* 3.4 50.0 + - + +
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Residues in contact with SER 69 (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 PHE* 3.1 46.1 - - - -
65A THR 3.3 4.8 + - - -
66A LEU* 2.7 20.4 + - - +
68A ASN* 1.3 81.6 + - - +
70A VAL* 1.3 67.1 + - - +
72A SER* 5.5 0.7 + - - -
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Residues in contact with VAL 70 (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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66A LEU 4.1 3.4 - - - +
67A VAL* 3.1 19.5 - - + +
68A ASN 3.9 0.2 - - - -
69A SER* 1.3 91.9 + - - +
71A ASN* 1.3 75.8 + - + +
72A SER* 4.2 1.5 + - - -
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Residues in contact with ASN 71 (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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67A VAL* 2.8 26.6 + - + +
68A ASN* 2.6 27.6 - - - +
70A VAL* 1.3 79.8 - - + +
72A SER* 1.3 76.3 + - - +
73A LYS* 2.7 20.2 + - - +
74A ILE* 3.3 29.0 + - - +
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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