Contacts of the helix formed by residues 48 - 62 (chain A) in PDB entry 1U61
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 SER 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR* 3.0 32.5 + - - -
45A SER* 5.0 0.5 - - - -
46A PHE 3.7 0.4 - - - -
47A VAL* 1.3 83.9 - - - +
49A ALA* 1.3 63.8 + - - +
50A LYS* 3.5 8.4 + - - +
51A ALA* 3.0 20.6 + - - +
52A GLN* 3.0 22.6 + - - +
96A SER* 4.5 0.4 - - - -
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Residues in contact with ALA 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 VAL 3.9 0.2 + - - -
48A SER* 1.3 73.4 - - - +
50A LYS* 1.3 58.3 + - + +
53A ALA* 2.9 32.1 + - - +
88A THR* 4.4 19.5 - - + -
92A THR* 3.6 14.4 - - + +
93A TYR* 4.6 9.2 - - + -
96A SER* 3.4 25.9 + - - +
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Residues in contact with LYS 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 SER* 3.3 7.7 + - - +
49A ALA* 1.3 79.7 - - + +
51A ALA* 1.3 61.7 + - - +
53A ALA* 3.8 1.6 - - - +
54A LYS* 3.1 23.7 + - - +
92A THR* 3.8 18.8 - - + +
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Residues in contact with ALA 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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45A SER 3.4 26.7 - - - +
46A PHE 3.8 14.6 - - - +
48A SER* 3.0 22.3 + - - +
50A LYS* 1.3 77.5 - - - +
52A GLN* 1.3 62.3 + - - +
54A LYS* 3.3 6.4 + - - +
55A VAL* 3.1 26.7 + - - +
126A LEU* 3.5 13.5 - - + +
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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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17A ASP* 5.5 2.8 + - - +
20A TYR* 3.2 31.5 - - + -
46A PHE 3.9 10.8 - - - +
47A VAL* 3.3 24.0 + - - +
48A SER 3.0 13.9 + - - +
51A ALA* 1.3 74.9 - - - +
53A ALA* 1.3 63.0 + - - +
55A VAL* 3.3 10.2 + - - +
56A VAL* 3.0 27.4 + - - +
96A SER* 2.9 38.7 + - - +
99A PHE* 3.8 23.3 - - + +
100A GLU* 3.0 24.3 + - - +
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Residues in contact with ALA 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 ALA 2.9 18.4 + - - +
50A LYS* 3.8 4.3 - - - +
51A ALA 3.3 0.2 - - - -
52A GLN* 1.3 74.7 - - - +
54A LYS* 1.3 60.2 + - - +
56A VAL* 3.0 3.2 + - - +
57A TYR* 2.8 49.4 + - + +
92A THR* 3.8 26.5 - - + +
95A HIS* 4.0 18.6 - - + -
96A SER* 4.3 1.5 - - - +
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Residues in contact with LYS 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 LYS 3.1 15.1 + - - +
51A ALA* 3.5 10.5 - - - +
53A ALA* 1.3 74.8 - - - +
55A VAL* 1.3 64.0 + - - +
57A TYR* 3.3 13.7 + - - +
58A HIS* 3.0 22.1 + - + +
125A VAL* 4.4 28.1 + - + -
126A LEU* 4.2 20.4 + - + +
128A GLU 5.1 6.3 + - - -
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Residues in contact with VAL 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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20A TYR* 5.0 1.3 - - - +
51A ALA 3.1 16.2 + - - +
52A GLN* 3.5 9.9 - - - +
53A ALA 3.2 0.2 - - - -
54A LYS* 1.3 75.3 - - - +
56A VAL* 1.3 57.6 + - - +
58A HIS* 3.2 8.1 + - - +
59A LEU* 2.9 41.8 + - + +
99A PHE* 3.7 20.2 - - + -
118A ILE 5.4 0.2 - - - +
122A ALA* 3.6 37.0 - - + +
125A VAL* 4.6 8.1 - - + -
126A LEU* 3.7 28.5 - - + -
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Residues in contact with VAL 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 GLN 3.0 15.5 + - - +
53A ALA 3.0 6.7 + - - +
55A VAL* 1.3 76.7 - - - +
57A TYR* 1.3 57.8 + - - +
59A LEU* 3.2 8.2 + - + +
60A LEU* 2.9 50.0 + - + +
73A LEU* 4.0 21.1 - - + -
95A HIS* 3.4 41.5 - - + +
98A ALA* 5.5 0.9 - - + -
99A PHE* 3.6 25.6 - - + +
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Residues in contact with TYR 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 ALA* 2.8 42.2 + - + +
54A LYS* 3.7 10.8 - - - +
56A VAL* 1.3 73.7 - - + +
58A HIS* 1.3 57.3 + - - +
60A LEU* 3.9 6.9 - - + +
61A GLU* 2.9 32.8 + - - +
91A GLN* 4.5 5.7 + - - +
92A THR* 4.5 9.3 + - - -
95A HIS* 3.6 45.5 - + - -
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Residues in contact with HIS 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 LYS* 3.0 14.2 + - + +
55A VAL 3.5 8.1 - - - +
57A TYR* 1.3 76.3 - - - +
59A LEU* 1.3 64.7 + - + +
61A GLU* 3.4 11.5 + - - +
62A THR* 2.9 57.9 + - + +
64A PHE* 6.2 0.4 - + + -
121A LYS* 4.5 21.0 - - + +
125A VAL* 3.7 41.1 - - + +
128A GLU* 5.4 6.2 + - - -
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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 VAL* 2.9 39.4 + - + +
56A VAL* 3.7 8.5 - - + +
58A HIS* 1.3 80.2 - - - +
60A LEU* 1.3 62.9 + - + +
62A THR* 3.9 3.1 - - - -
63A ALA* 3.2 4.0 + - - -
64A PHE* 3.2 58.9 + - + -
65A LEU* 4.0 34.8 + - + +
70A GLU* 4.9 0.7 - - - +
73A LEU* 5.4 1.6 - - + -
99A PHE* 4.7 7.0 - - + -
102A LEU* 4.9 3.1 - - + -
118A ILE* 4.5 16.2 - - + +
121A LYS* 3.9 20.2 - - + -
125A VAL* 6.0 0.4 - - + -
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Residues in contact with LEU 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 VAL* 2.9 38.3 + - + +
57A TYR* 3.9 8.5 - - + +
59A LEU* 1.3 74.0 - - - +
61A GLU* 1.3 65.0 + - - +
63A ALA* 3.4 10.6 + - - +
65A LEU* 4.9 0.4 - - + -
70A GLU* 3.9 32.7 - - + +
73A LEU* 3.8 22.0 - - + -
95A HIS* 4.8 14.1 - - + +
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Residues in contact with GLU 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 TYR 2.9 18.0 + - - +
58A HIS* 3.7 13.2 - - - +
59A LEU 3.4 0.2 - - - -
60A LEU* 1.3 80.1 - - - +
62A THR* 1.3 70.2 + - - +
63A ALA* 3.6 1.2 + - - +
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Residues in contact with THR 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 HIS* 2.9 45.9 + - + +
59A LEU 3.5 5.5 + - - -
61A GLU* 1.3 88.6 - - - +
63A ALA* 1.3 69.1 + - - +
64A PHE* 3.2 15.6 + - - +
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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