Contacts of the helix formed by residues 41 - 61 (chain A) in PDB entry 1UK0
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 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 2.7 13.1 + - - +
40A LEU* 1.3 81.0 - - - +
42A LYS* 1.3 59.2 + - - +
43A ARG* 3.9 20.7 - - - +
44A GLN* 3.0 33.7 + - - +
45A ILE* 2.8 36.5 + - - +
111A GLU* 4.6 1.1 - - - -
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Residues in contact with LYS 42 (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 SER* 1.3 70.5 - - - +
43A ARG* 1.3 91.7 + - - +
45A ILE* 3.5 10.1 + - + +
46A GLN* 2.6 51.8 + - - +
108A LEU* 5.0 8.3 - - + +
111A GLU* 3.9 28.7 - - + +
115A SER* 5.7 2.0 - - - -
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Residues in contact with ARG 43 (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 SER* 3.9 15.5 - - - +
42A LYS* 1.3 124.7 - - - +
44A GLN* 1.4 66.6 + - - +
46A GLN* 2.9 32.2 + - - +
47A ALA* 3.1 12.8 + - - +
111A GLU* 5.6 1.0 + - - -
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Residues in contact with GLN 44 (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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35A MET* 3.4 33.7 - - - +
39A LYS* 3.7 18.7 - - + +
40A LEU* 4.1 6.8 - - - +
41A SER* 3.0 40.7 + - - +
43A ARG* 1.4 77.8 - - - +
45A ILE* 1.3 64.0 + - - +
47A ALA* 3.7 7.3 - - - +
48A ALA* 3.2 20.1 + - - +
78A LEU* 2.9 46.1 + - + +
79A ILE* 3.8 8.0 - - - +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.3 9.2 - - + -
41A SER 2.8 35.9 + - - +
42A LYS* 3.7 4.3 - - - +
44A GLN* 1.3 80.3 + - - +
46A GLN* 1.3 68.0 + - - +
48A ALA* 3.1 14.6 + - - +
49A TYR* 3.2 21.1 + - + -
79A ILE* 4.7 1.8 - - + -
104A LEU* 3.6 29.2 - - + +
107A LEU* 3.6 30.3 - - + +
108A LEU* 3.5 34.8 - - + -
111A GLU* 4.3 11.0 - - + -
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Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 2.6 35.2 + - - +
43A ARG* 2.9 20.7 + - - +
45A ILE* 1.3 69.8 - - - +
47A ALA* 1.4 55.3 + - - +
49A TYR* 2.7 41.2 + - + +
50A SER* 3.3 9.6 + - - -
108A LEU* 5.4 2.0 - - + +
220A PRO* 5.3 5.4 - - + +
222A GLU* 3.8 30.0 + - - +
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Residues in contact with ALA 47 (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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43A ARG 3.1 10.3 + - - +
44A GLN* 3.7 6.5 - - - +
46A GLN* 1.4 77.4 - - - +
48A ALA* 1.3 57.1 + - - +
49A TYR 3.3 0.2 + - - -
50A SER* 3.4 10.1 + - - -
51A ILE* 3.1 30.0 + - + +
78A LEU* 3.6 24.2 - - + -
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Residues in contact with ALA 48 (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 GLN 3.2 4.1 + - - +
45A ILE 3.1 10.5 + - - +
47A ALA* 1.3 79.5 - - - +
49A TYR* 1.4 58.0 + - - +
51A ILE* 3.6 4.5 + - - +
52A LEU* 3.0 32.2 + - - +
75A PHE* 4.1 6.5 - - + -
78A LEU* 3.4 9.4 - - + +
79A ILE* 3.6 37.2 - - + -
104A LEU* 3.7 14.6 - - + -
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Residues in contact with TYR 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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45A ILE* 3.2 29.2 + - + -
46A GLN* 2.7 23.6 + - + +
48A ALA* 1.4 71.2 - - - +
50A SER* 1.3 53.5 + - - +
52A LEU* 3.6 1.7 + - + -
53A SER* 2.7 30.8 + - - -
101A VAL* 4.0 12.8 - - + -
104A LEU* 3.6 27.1 - - + -
105A ASP* 2.7 36.1 + - - -
108A LEU* 3.2 29.7 - - + +
220A PRO* 3.3 30.9 - - + +
222A GLU* 3.0 25.5 - - + +
223A ALA* 3.4 23.3 - - + -
224A PRO* 3.6 6.1 - - + +
228A TYR* 3.9 4.0 - - - -
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLN 3.3 10.6 + - - -
47A ALA* 3.4 10.3 + - - -
49A TYR* 1.3 77.6 - - - +
51A ILE* 1.3 60.1 + - - +
53A SER* 3.8 2.8 - - - +
54A GLU* 2.6 43.1 + - - +
222A GLU* 3.6 23.2 + - - +
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Residues in contact with ILE 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 ALA* 3.1 14.5 + - + +
48A ALA* 3.6 3.8 + - - +
49A TYR 3.5 0.2 - - - -
50A SER* 1.3 74.1 - - - +
52A LEU* 1.4 66.7 + - - +
54A GLU* 2.9 27.0 + - - +
55A VAL* 2.9 12.6 + - + +
71A LEU* 3.4 48.7 - - + +
74A ARG* 3.9 34.1 - - + +
75A PHE* 4.1 8.5 - - + +
78A LEU* 3.8 26.5 - - + -
43B ARG* 5.4 4.3 - - + -
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Residues in contact with LEU 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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48A ALA 3.0 15.0 + - - +
49A TYR* 4.0 2.7 - - - +
51A ILE* 1.4 70.0 - - - +
53A SER* 1.4 62.2 + - - +
55A VAL* 3.4 9.5 + - + +
56A GLN* 3.2 19.2 + - - +
75A PHE* 3.4 33.2 - - + -
91A LEU* 4.1 11.9 - - + -
97A VAL* 3.5 28.9 - - + +
100A LYS* 4.0 22.7 - - + -
101A VAL* 4.1 11.4 - - + +
104A LEU* 3.5 31.2 - - + -
224A PRO* 3.9 16.2 - - + +
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR 2.7 22.6 + - - -
50A SER* 3.8 4.0 - - - -
51A ILE 3.0 0.8 + - - -
52A LEU* 1.4 70.8 - - - +
54A GLU* 1.4 56.7 - - - +
56A GLN* 2.7 25.0 + - - +
57A GLN* 3.2 11.3 + - - +
222A GLU 3.7 13.2 - - - -
223A ALA 4.7 0.7 - - - -
224A PRO* 3.8 20.9 - - - +
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Residues in contact with GLU 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 SER* 2.6 39.3 + - - +
51A ILE* 2.9 23.7 + - - +
53A SER* 1.4 69.5 - - - +
55A VAL* 1.3 63.5 + - - +
56A GLN 2.8 1.4 + - - -
57A GLN* 3.3 10.8 + - - +
58A ALA* 3.4 12.0 + - - +
71A LEU* 3.3 35.3 - - + +
74A ARG* 4.6 3.8 + - - -
43B ARG* 3.9 41.0 + - - +
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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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51A ILE* 2.9 12.7 + - + +
52A LEU* 3.9 5.4 - - + +
53A SER 3.3 0.2 - - - -
54A GLU* 1.3 72.5 - - - +
56A GLN* 1.4 63.5 + - + +
58A ALA* 3.8 0.5 - - - -
59A VAL* 2.8 36.9 + - + +
68A ILE* 3.5 11.9 - - + +
71A LEU* 3.4 35.0 - - + -
72A SER 4.5 0.4 - - - +
91A LEU* 3.1 47.1 - - + +
93A ASN 5.7 0.7 - - - +
97A VAL* 3.8 28.5 - - + -
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Residues in contact with GLN 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 LEU 3.2 8.7 + - - +
53A SER* 2.7 17.3 + - - +
55A VAL* 1.4 78.2 - - + +
57A GLN* 1.4 70.2 + - - +
59A VAL* 2.9 12.0 + - + -
60A SER* 3.1 20.1 + - - +
93A ASN 4.6 1.1 + - - +
94A ALA* 3.9 19.6 - - - +
97A VAL* 3.6 29.3 - - + +
98A GLN* 3.9 1.8 + - - -
224A PRO* 3.7 15.7 - - + +
226A THR* 2.8 51.6 + - + +
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Residues in contact with GLN 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 SER 3.2 9.6 + - - +
54A GLU* 4.2 5.6 - - - +
56A GLN* 1.4 79.2 - - - +
58A ALA* 1.3 58.8 + - - +
60A SER* 3.0 2.1 + - - -
61A GLN* 2.7 82.4 + - - +
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Residues in contact with ALA 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 GLU 3.4 11.3 + - - +
56A GLN 3.1 0.2 - - - -
57A GLN* 1.3 86.1 - - + +
59A VAL* 1.3 69.3 + - - +
61A GLN 3.1 11.7 - - - -
62A GLY 3.0 18.5 - - - +
63A SER* 3.4 27.8 - - - +
67A GLN* 5.2 2.9 - - + -
68A ILE* 3.9 16.4 - - + -
71A LEU* 5.0 3.1 - - + -
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Residues in contact with VAL 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* 2.8 29.0 + - + +
56A GLN* 2.9 5.7 + - + +
57A GLN 2.8 4.6 + - - -
58A ALA* 1.3 81.4 - - - +
60A SER* 1.3 63.3 - - - +
61A GLN 3.2 0.2 + - - -
62A GLY* 3.5 12.8 + - - +
68A ILE* 4.2 12.6 - - + -
91A LEU 3.6 7.9 - - - +
92A ASN* 3.4 47.1 - - + +
93A ASN* 4.3 6.7 - - - +
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Residues in contact with SER 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 GLN* 3.1 16.2 + - - +
57A GLN 3.0 4.4 + - - -
59A VAL* 1.3 75.8 - - - +
61A GLN* 1.3 78.2 + - - +
62A GLY 3.5 3.8 + - - -
226A THR* 6.0 1.6 - - - +
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 2.7 60.8 + - - +
58A ALA* 3.1 6.9 - - - +
60A SER* 1.3 92.4 + - - +
62A GLY* 1.4 50.4 - - - +
63A SER* 2.7 22.3 + - - -
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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
------------------------------------------------------------
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