Contacts of the helix formed by residues 61 - 73 (chain P) in PDB entry 3UCU
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 61 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P HIS* 4.1 3.8 - - - -
39P GLN* 4.4 13.3 - - - +
59P PHE* 3.4 6.6 - - - +
60P LYS* 1.3 90.6 - - + +
62P VAL* 1.3 63.3 + - - +
63P SER* 3.6 20.9 + - - +
64P SER* 2.6 33.1 + - - +
65P ALA 3.3 3.8 + - - -
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Residues in contact with VAL 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PRO* 3.8 28.9 - - + +
9P ASN* 3.8 16.2 - - - +
10P HIS* 3.5 42.4 + - + +
61P GLU* 1.3 69.8 - - - +
63P SER* 1.3 53.8 + - - +
65P ALA* 3.0 8.3 + - - +
66P THR* 2.7 42.2 + - - +
86P TYR* 5.0 0.4 - - + -
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Residues in contact with SER 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P GLU* 3.6 22.4 + - - +
62P VAL* 1.3 80.0 - - - +
64P SER* 1.3 58.6 + - - +
66P THR* 3.2 9.2 + - - -
67P ASN* 3.0 38.7 + - - +
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Residues in contact with SER 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P PHE* 3.1 36.7 - - - +
38P GLY* 3.9 7.0 - - - -
39P GLN 5.2 0.2 + - - -
59P PHE* 3.3 18.3 - - - +
60P LYS 4.8 0.2 + - - -
61P GLU* 2.6 32.1 + - - +
63P SER* 1.3 78.8 + - - +
65P ALA* 1.3 59.0 + - - +
67P ASN* 3.6 5.9 + - - +
68P ALA* 3.2 27.0 + - - +
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Residues in contact with ALA 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P ASN 3.4 22.4 - - - +
10P HIS 3.6 6.3 - - - +
12P ILE* 3.7 15.1 - - + +
59P PHE* 3.5 28.5 - - + -
61P GLU 3.3 4.5 + - - +
62P VAL 3.0 9.5 + - - +
64P SER* 1.3 80.4 + - - +
66P THR* 1.3 63.7 + - - +
68P ALA* 3.5 0.7 + - - +
69P LEU* 3.2 24.3 + - - +
86P TYR* 4.6 2.4 - - + -
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Residues in contact with THR 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P PRO* 4.8 1.4 - - - +
62P VAL* 2.7 30.5 + - - +
63P SER* 3.2 12.6 + - - -
65P ALA* 1.3 73.8 - - - +
67P ASN* 1.3 68.3 + - - +
69P LEU* 3.6 2.1 + - - +
70P ARG* 3.2 58.0 + - - +
86P TYR* 2.9 27.0 + - - +
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Residues in contact with ASN 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P PHE* 4.1 15.0 + - + +
63P SER* 3.0 18.8 + - - +
64P SER* 4.0 7.5 - - - +
65P ALA 3.3 0.2 - - - -
66P THR* 1.3 80.2 - - - +
68P ALA* 1.3 55.0 + - - +
70P ARG* 3.3 6.1 + - - +
71P SER* 2.7 46.0 + - - +
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Residues in contact with ALA 68 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P ILE* 4.5 2.5 - - + -
34P PHE* 4.0 11.4 - - + -
37P PHE* 3.7 31.8 - - + -
59P PHE* 3.8 19.3 - - + -
64P SER 3.2 16.0 + - - +
65P ALA 3.8 4.9 - - - +
67P ASN* 1.3 77.5 - - - +
69P LEU* 1.3 62.5 + - - +
72P MET* 3.2 26.3 + - - +
84P ILE* 3.9 5.3 - - - +
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Residues in contact with LEU 69 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P ARG* 6.2 0.2 - - - +
12P ILE* 4.5 2.7 - - + +
65P ALA 3.2 16.3 + - - +
66P THR* 3.8 4.9 - - - +
68P ALA* 1.3 76.8 - - - +
70P ARG* 1.3 78.9 + - + +
73P GLN* 3.1 37.5 + - + +
84P ILE* 3.8 31.8 - - + +
85P GLN* 3.8 11.7 - - - +
86P TYR* 3.8 53.8 - - + +
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Residues in contact with ARG 70 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P THR* 3.2 43.4 + - - +
67P ASN* 4.1 5.6 + - - +
69P LEU* 1.3 93.4 - - + +
71P SER* 1.3 61.4 + - - +
73P GLN* 4.4 6.1 + - - +
86P TYR* 5.6 0.4 - - - -
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Residues in contact with SER 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P ARG* 5.6 2.7 - - - -
37P PHE* 3.6 23.6 - - - -
67P ASN* 2.7 34.2 + - - +
70P ARG* 1.3 75.1 - - - +
72P MET* 1.3 62.5 + - - +
73P GLN 3.8 0.7 - - - -
75P PHE* 5.6 1.0 - - - -
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Residues in contact with MET 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P ILE* 3.7 35.7 - - + +
34P PHE* 4.5 9.9 - - + -
36P ARG* 3.4 25.8 - - - +
37P PHE* 3.7 22.0 - - + -
68P ALA 3.2 15.5 + - - +
71P SER* 1.3 84.0 - - - +
73P GLN* 1.4 63.7 + - - +
74P GLY 3.5 1.4 + - - -
75P PHE* 3.4 52.0 + - + +
82P MET* 4.3 5.4 - - + +
84P ILE* 3.2 18.7 - - + +
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Residues in contact with GLN 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P LEU* 3.1 25.3 + - + +
70P ARG* 4.4 5.5 + - - +
71P SER 3.8 1.6 - - - -
72P MET* 1.4 76.2 - - - +
74P GLY* 1.3 82.0 + - - +
75P PHE 3.3 3.1 + - - -
82P MET 3.7 3.3 - - - +
83P ARG* 3.7 15.2 + - - +
84P ILE* 2.8 50.9 + - + +
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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