Contacts of the helix formed by residues 53 - 70 (chain A) in PDB entry 1UPH
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLY 4.6 0.2 - - - +
50A LEU* 3.2 16.0 + - - +
51A LEU 3.8 0.5 - - - +
52A GLU* 1.3 96.8 - - + +
54A SER* 1.3 64.5 + - - +
55A GLU* 2.9 10.0 + - - +
56A GLY* 3.0 16.3 + - - -
57A CYS* 3.0 19.8 + - - +
89A HIS* 3.9 0.4 - - - -
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU 3.6 2.6 + - - -
53A THR* 1.3 71.4 - - - +
55A GLU* 1.3 58.3 + - - +
57A CYS* 3.8 0.4 - - - -
58A ARG* 2.9 23.9 + - - +
86A TYR* 3.1 16.9 - - - -
89A HIS* 3.2 41.2 + - - +
90A GLN* 3.7 31.6 + - - -
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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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53A THR* 2.9 8.4 - - - +
54A SER* 1.3 77.7 - - - +
56A GLY* 1.3 55.6 + - - +
58A ARG* 3.1 8.6 + - + +
59A GLN* 2.7 44.2 + - + +
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.5 33.5 - - - +
51A LEU* 4.6 0.2 - - - -
53A THR* 3.0 11.3 + - - -
55A GLU* 1.3 76.8 - - - +
57A CYS* 1.3 57.0 + - - +
59A GLN* 3.3 10.9 + - - +
60A ILE* 2.9 39.7 + - - +
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Residues in contact with CYS 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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51A LEU* 3.5 23.4 + - + -
53A THR 3.0 14.4 + - - +
54A SER 3.8 1.8 - - - +
56A GLY* 1.3 75.6 - - - +
58A ARG* 1.3 59.8 + - - +
60A ILE 3.3 0.7 + - - -
61A LEU* 3.0 25.9 + - - +
82A ILE* 2.8 55.1 - - - +
85A LEU* 3.6 11.9 - - - -
86A TYR* 3.4 21.3 - - + -
89A HIS* 3.8 9.2 - - + -
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Residues in contact with ARG 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 SER 2.9 19.5 + - - +
55A GLU* 3.1 8.9 + - - +
57A CYS* 1.3 74.4 - - - +
59A GLN* 1.3 64.8 + - - +
61A LEU* 3.4 8.4 + - + +
62A GLY* 2.9 35.3 + - - -
65A GLN* 4.5 5.1 - - - +
86A TYR* 3.4 29.3 + - + -
108A GLN* 3.8 38.8 + - - +
111A SER* 5.9 3.2 + - - -
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Residues in contact with GLN 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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50A LEU* 5.3 4.6 - - + +
55A GLU* 2.7 26.2 + - + +
56A GLY* 3.5 12.8 - - - +
58A ARG* 1.3 76.4 - - + +
60A ILE* 1.3 55.4 + - + +
62A GLY* 3.0 3.2 + - - -
63A GLN* 2.7 47.8 + - - +
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Residues in contact with ILE 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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41A LEU* 3.4 30.7 - - + -
44A PHE* 6.3 1.3 - - + -
46A VAL* 3.9 24.5 - - + -
50A LEU* 5.1 2.5 - - + -
51A LEU* 3.4 26.2 - - + -
56A GLY* 2.9 26.3 + - - +
57A CYS* 3.3 3.6 + - - +
59A GLN* 1.3 76.0 - - + +
61A LEU* 1.3 58.3 + - - +
63A GLN* 2.8 28.9 + - + +
64A LEU* 2.8 23.9 + - + +
82A ILE* 3.4 30.5 - - + -
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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 CYS 3.0 17.3 + - - +
58A ARG* 3.6 8.7 - - + +
59A GLN 3.2 0.2 - - - -
60A ILE* 1.3 77.2 - - - +
62A GLY* 1.3 50.9 + - - +
64A LEU* 3.3 1.2 + - - -
65A GLN* 2.4 48.1 + - - +
79A TYR* 2.6 73.3 - - + +
82A ILE* 4.2 4.7 - - + +
83A ALA* 3.5 23.3 - - + +
86A TYR* 5.6 2.9 - - + -
104A ILE* 3.6 34.8 - - + -
108A GLN* 4.6 6.7 - - - +
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Residues in contact with GLY 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 ARG* 2.9 21.9 + - - -
59A GLN* 3.0 4.9 + - - -
61A LEU* 1.3 75.8 - - - +
63A GLN* 1.3 59.1 + - - +
65A GLN* 3.2 22.3 + - - +
66A PRO* 3.1 21.3 - - - +
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Residues in contact with GLN 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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46A VAL* 5.1 14.2 - - - +
59A GLN* 2.7 25.9 + - - +
60A ILE* 2.8 18.5 + - - +
62A GLY* 1.3 81.0 - - - +
64A LEU* 1.3 64.3 + - + +
66A PRO* 3.3 14.2 - - - +
67A SER* 3.5 11.3 + - - -
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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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44A PHE* 4.0 26.9 - - + -
60A ILE* 2.8 23.0 + - + +
63A GLN* 1.3 88.4 - - + +
65A GLN* 1.3 66.8 + - - +
66A PRO* 3.1 3.8 - - - -
67A SER* 2.7 16.9 + - - +
68A LEU* 2.6 32.2 + - + +
75A LEU* 4.1 29.4 - - + +
78A LEU* 5.1 4.9 - - + -
79A TYR* 4.1 17.7 - - + +
82A ILE* 4.1 24.2 - - + -
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Residues in contact with GLN 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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58A ARG* 4.5 7.3 - - - +
61A LEU* 2.4 42.2 + - - +
62A GLY* 3.3 19.8 - - - +
64A LEU* 1.3 79.1 - - - +
66A PRO* 1.4 63.8 - - + +
68A LEU* 3.2 25.3 - - + +
69A GLN* 3.9 2.6 + - - +
79A TYR* 3.2 20.8 + - + +
108A GLN* 4.2 26.6 - - - +
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Residues in contact with PRO 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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62A GLY 3.1 12.3 - - - +
63A GLN* 3.3 9.9 - - - +
64A LEU 3.1 4.7 - - - -
65A GLN* 1.4 95.7 - - + +
67A SER* 1.3 54.5 + - - +
68A LEU 2.8 4.7 - - - -
69A GLN* 2.8 39.0 + - + +
70A THR* 4.1 1.9 + - - +
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Residues in contact with SER 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 GLN 3.5 13.0 + - - -
64A LEU* 2.7 26.2 + - - +
66A PRO* 1.3 76.0 - - - +
68A LEU* 1.3 50.5 + - - +
70A THR* 3.4 6.2 - - - +
71A GLY* 2.6 37.8 + - - -
75A LEU* 3.8 16.8 - - - -
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Residues in contact with LEU 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 LEU* 2.6 20.8 + - + +
65A GLN* 3.2 17.0 - - + +
66A PRO 2.8 0.2 - - - -
67A SER* 1.3 75.9 - - - +
69A GLN* 1.3 66.2 + - - +
70A THR* 2.7 4.5 + - - -
71A GLY* 3.0 11.8 + - - +
75A LEU* 4.6 3.1 - - + +
76A ARG* 3.3 57.0 + - + +
79A TYR* 2.8 68.9 - - + -
80A ASN* 5.4 0.2 - - - +
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Residues in contact with GLN 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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65A GLN 3.9 2.4 + - - +
66A PRO* 2.8 22.0 + - + +
68A LEU* 1.3 78.9 - - - +
70A THR* 1.3 62.4 + - + +
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Residues in contact with THR 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 PRO 5.2 2.0 - - - +
67A SER* 3.4 5.9 + - - +
68A LEU 2.7 0.4 + - - -
69A GLN* 1.3 82.8 - - + +
71A GLY* 1.3 65.5 + - - +
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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