Contacts of the helix formed by residues 30 - 52 (chain A) in PDB entry 1U1H
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.7 9.5 - - - -
29A SER* 1.3 78.3 + - - +
31A ALA* 1.3 64.8 + - - +
32A GLU* 3.3 11.0 + - - +
33A ASP* 2.8 43.7 + - - +
34A LEU* 3.3 9.0 + - - +
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Residues in contact with ALA 31 (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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24A PHE* 3.7 23.8 - - + -
30A THR* 1.3 75.4 - - - +
32A GLU* 1.3 66.0 + - + +
34A LEU* 3.1 6.1 + - - +
35A GLN* 3.0 28.1 + - + +
91A LEU* 4.1 15.6 - - + +
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 3.2 8.4 + - - +
31A ALA* 1.3 79.4 - - + +
33A ASP* 1.3 59.6 + - - +
35A GLN* 3.0 10.1 + - - +
36A LYS* 2.8 31.5 + - - +
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 3.8 15.6 - - - -
30A THR* 2.8 42.9 + - - +
32A GLU* 1.3 77.4 - - - +
34A LEU* 1.3 61.7 + - - +
36A LYS* 3.5 7.9 + - - +
37A VAL* 3.2 27.2 + - - +
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.3 4.5 - - + -
20A ALA* 4.1 25.8 - - + +
21A LEU* 4.2 13.0 - - + -
24A PHE* 3.9 31.9 - - + -
29A SER* 5.5 0.8 + - - -
30A THR 3.3 8.5 + - - +
31A ALA 3.1 9.7 + - - +
33A ASP* 1.3 75.7 - - - +
35A GLN* 1.3 61.4 + - - +
37A VAL* 3.2 5.6 + - - +
38A SER* 2.8 44.2 + - - +
64A HIS* 4.1 12.3 - - + +
91A LEU* 3.9 25.4 - - + -
95A PHE* 4.1 15.3 - - + -
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Residues in contact with GLN 35 (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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31A ALA* 3.0 23.1 + - + +
32A GLU* 3.0 9.6 + - - +
34A LEU* 1.3 75.6 - - + +
36A LYS* 1.3 55.4 + - - +
38A SER* 3.5 5.4 - - - -
39A ALA* 2.7 38.8 + - - +
42A ARG* 5.0 8.1 + - - +
64A HIS* 3.9 28.5 + - - -
91A LEU* 4.2 18.0 - - + +
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Residues in contact with LYS 36 (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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32A GLU 2.8 15.1 + - - +
33A ASP* 3.6 9.0 - - - +
35A GLN* 1.3 77.2 - - - +
37A VAL* 1.3 64.4 + - + +
39A ALA* 4.0 5.5 - - + +
40A ASP* 2.8 57.4 + - - +
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Residues in contact with VAL 37 (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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16A GLU* 4.3 24.7 - - + +
17A LEU* 4.5 7.2 - - + +
20A ALA* 3.7 28.9 - - + -
33A ASP 3.2 12.7 + - - +
34A LEU 3.2 7.2 + - - +
36A LYS* 1.3 80.4 - - + +
38A SER* 1.3 63.5 + - - +
40A ASP* 4.1 4.8 - - - +
41A LEU* 3.2 24.1 + - + +
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Residues in contact with SER 38 (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 LEU* 3.9 3.1 - - - +
34A LEU* 2.8 29.1 + - - +
35A GLN* 3.1 10.1 + - - -
37A VAL* 1.3 76.7 - - - +
39A ALA* 1.3 65.1 + - - +
41A LEU* 3.3 4.6 + - - +
42A ARG* 3.1 36.7 + - - +
62A PHE* 3.5 25.4 - - - -
64A HIS* 3.0 24.3 + - - -
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Residues in contact with ALA 39 (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 GLN 2.7 20.1 + - - +
36A LYS* 4.2 5.6 - - + +
38A SER* 1.3 71.2 - - - +
40A ASP* 1.3 68.5 + - - +
42A ARG* 3.2 16.4 + - - +
43A SER* 3.0 24.5 + - - -
143A GLU* 3.7 20.6 - - - +
147A LEU* 5.5 0.2 - - - +
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Residues in contact with ASP 40 (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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36A LYS* 2.8 57.9 + - - +
37A VAL* 4.1 4.8 - - - +
39A ALA* 1.3 78.3 - - - +
41A LEU* 1.3 57.9 + - - +
43A SER* 3.4 8.3 + - - -
44A SER* 2.9 31.2 + - - -
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Residues in contact with LEU 41 (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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10A ARG* 3.5 26.5 - - - +
11A MSE 4.2 4.3 - - - +
12A GLY* 3.9 28.0 - - - +
13A PRO* 4.5 8.5 - - + -
16A GLU* 4.5 11.0 - - + +
17A LEU* 4.2 17.3 - - + +
37A VAL 3.2 17.2 + - - +
38A SER* 3.5 6.7 - - - +
39A ALA 3.2 0.2 - - - -
40A ASP* 1.3 80.7 - - - +
42A ARG* 1.3 57.3 + - - +
44A SER* 3.5 7.2 + - - -
45A ILE* 2.9 47.9 + - + +
62A PHE* 4.7 9.6 - - + -
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Residues in contact with ARG 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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35A GLN* 5.0 8.3 + - - +
38A SER* 3.1 25.1 + - - +
39A ALA* 3.2 18.8 + - - +
41A LEU* 1.3 74.7 - - - +
43A SER* 1.3 59.9 + - - +
45A ILE* 3.2 7.4 + - - +
46A TRP* 2.9 53.8 + - + -
62A PHE* 3.5 47.5 - - + -
64A HIS* 5.2 1.0 + - - -
140A GLU* 3.5 36.3 + - - +
143A GLU* 2.7 39.3 + - - -
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Residues in contact with SER 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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39A ALA 3.0 16.5 + - - -
40A ASP* 3.6 9.4 - - - -
42A ARG* 1.3 75.9 - - - +
44A SER* 1.3 57.2 + - - +
46A TRP* 3.4 1.9 + - - +
47A LYS* 2.9 51.1 + - - +
147A LEU* 3.5 36.3 - - - +
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Residues in contact with SER 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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13A PRO* 6.2 0.2 - - - +
40A ASP 2.9 17.9 + - - -
41A LEU* 3.5 12.3 - - - -
43A SER* 1.3 76.9 - - - +
45A ILE* 1.3 59.2 + - - +
47A LYS* 4.1 4.1 - - - +
48A GLN* 3.0 33.7 + - - +
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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
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8A TYR* 3.3 46.4 - - + -
9A PRO 4.5 6.7 - - - +
10A ARG* 6.1 0.7 - - - -
12A GLY* 6.0 2.0 - - - -
13A PRO* 5.9 4.7 - - + -
41A LEU* 2.9 43.6 + - + +
42A ARG* 3.7 7.0 - - - +
44A SER* 1.3 76.7 - - - +
46A TRP* 1.3 67.4 + - + +
48A GLN* 3.2 13.6 + - - +
49A MSE 3.0 50.3 + - + +
335A VAL* 5.9 2.2 - - + -
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Residues in contact with TRP 46 (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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42A ARG* 2.9 43.7 + - + +
43A SER* 3.8 2.5 - - - +
45A ILE* 1.3 78.2 - - + +
47A LYS* 1.3 58.5 + - + +
49A MSE 3.4 8.1 + - + +
50A SER* 2.9 29.0 + - - -
57A ILE* 3.9 17.4 - - + +
58A PRO 3.1 25.8 + - - -
59A SER* 4.0 7.6 - - - +
140A GLU* 3.5 39.3 - - + -
143A GLU* 3.2 31.4 - - - -
144A ALA* 3.5 26.5 - - + -
147A LEU* 3.6 15.9 - - + -
149A VAL* 3.5 23.8 - - + +
151A THR* 3.9 5.9 - - + +
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Residues in contact with LYS 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 SER* 2.9 40.1 + - - +
44A SER* 4.2 3.8 - - - +
46A TRP* 1.3 71.2 - - + +
48A GLN* 1.3 59.8 + - - +
50A SER* 3.5 7.0 - - - -
51A ALA* 2.8 34.6 + - - +
147A LEU* 4.1 30.5 + - + +
149A VAL* 5.5 4.5 - - + -
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Residues in contact with GLN 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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8A TYR* 3.0 37.0 + - - -
44A SER* 3.0 19.6 + - - +
45A ILE* 3.3 17.4 - - - +
47A LYS* 1.3 80.0 - - - +
49A MSE 1.3 63.4 + - - +
51A ALA* 3.5 4.7 + - - +
52A ALA* 3.2 19.6 + - - +
335A VAL* 6.1 0.2 - - - +
336A ASP* 6.0 0.4 - - - -
355A ALA* 3.7 24.6 + - - +
358A VAL* 4.5 9.6 - - + +
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Residues in contact with MSE 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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5A ILE* 3.6 35.0 - - + -
8A TYR* 4.3 14.1 - - + -
45A ILE* 3.0 45.4 + - + +
46A TRP* 3.9 8.5 - - + +
48A GLN* 1.3 79.2 - - - +
50A SER* 1.3 64.0 + - - +
52A ALA* 3.3 8.0 + - - +
54A THR* 2.7 32.6 + - - +
57A ILE* 3.6 29.2 - - + -
58A PRO* 3.9 28.9 - - + +
61A THR* 5.7 0.4 - - - +
358A VAL* 4.1 15.7 - - + -
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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
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46A TRP 2.9 18.2 + - - -
47A LYS* 3.2 8.5 + - - -
49A MSE 1.3 76.0 - - - +
51A ALA* 1.3 66.8 + - - +
53A GLY* 2.9 17.0 + - - -
54A THR 4.1 3.2 + - - +
57A ILE* 3.5 17.4 - - - +
148A GLY 5.4 1.2 + - - -
149A VAL* 3.9 15.4 - - - +
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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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47A LYS 2.8 19.8 + - - +
48A GLN* 3.9 4.7 - - - +
50A SER* 1.3 73.3 - - - +
52A ALA* 1.3 59.4 + - - +
53A GLY* 3.4 1.0 + - - -
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Residues in contact with ALA 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 GLN 3.2 13.2 + - - +
49A MSE 3.4 12.1 - - - +
50A SER 3.0 0.6 + - - -
51A ALA* 1.3 77.0 - - - +
53A GLY* 1.3 57.0 + - - +
358A VAL* 3.9 15.7 - - + +
359A VAL* 5.2 10.1 - - + -
362A ASN* 3.2 31.9 - - + +
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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
------------------------------------------------------------
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