Contacts of the helix formed by residues 15 - 34 (chain A) in PDB entry 1UI9
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 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 3.1 22.3 + - + +
14A ASP* 1.3 82.4 + - - +
16A PRO* 1.3 75.8 - - + +
17A GLU* 3.6 12.6 + - - +
18A ALA* 3.1 25.1 + - - +
19A ILE* 3.1 26.1 + - - +
55A PHE* 4.5 0.7 - - - +
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Residues in contact with PRO 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 1.3 87.3 - - - +
17A GLU* 1.3 69.4 + - - +
19A ILE* 3.4 3.1 + - + +
20A HIS* 2.8 32.0 + - - +
55A PHE* 3.3 47.8 - - + +
57A PHE* 4.3 18.2 + - + -
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 3.6 18.1 - - - +
16A PRO* 1.3 90.8 - - - +
18A ALA* 1.3 61.8 + - - +
20A HIS* 3.3 6.3 + - - +
21A GLN* 3.0 25.3 + - - +
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.5 11.5 - - + +
12A GLU 5.5 0.7 - - - +
13A GLU* 3.5 27.6 - - + +
15A THR* 3.1 20.6 + - - +
17A GLU* 1.3 76.0 - - - +
19A ILE* 1.3 62.1 + - - +
21A GLN* 4.0 6.6 - - - +
22A ALA* 3.1 25.6 + - - +
109A ARG* 5.1 0.7 + - - -
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.0 11.7 - - + -
14A ASP* 4.0 18.2 - - - +
15A THR 3.1 19.1 + - - +
16A PRO* 3.7 4.5 - - + +
18A ALA* 1.3 77.7 - - - +
20A HIS* 1.3 59.6 + - - +
22A ALA* 3.9 1.0 - - - +
23A THR* 2.8 37.5 + - - +
53A LEU* 4.0 26.2 - - + -
54A THR 4.6 0.2 - - - +
55A PHE 3.6 20.2 - - - +
56A ALA* 3.7 32.8 - - + -
57A PHE 4.4 5.8 - - - +
58A PRO 4.9 3.4 - - - -
88A ILE* 4.0 17.0 - - + -
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Residues in contact with HIS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO 2.8 18.5 + - - +
17A GLU* 3.5 7.9 - - - +
19A ILE* 1.3 78.9 - - - +
21A GLN* 1.3 63.7 + - + +
23A THR* 4.7 0.4 - - - -
24A ARG* 3.0 40.2 + - - +
57A PHE* 4.7 8.1 + - + +
60A GLU* 3.6 20.9 - - + +
61A ALA* 3.4 37.3 + - + +
64A GLN* 2.9 29.9 + - + -
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Residues in contact with GLN 21 (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 GLU 3.0 13.8 + - - +
18A ALA* 4.0 6.3 - - - +
20A HIS* 1.3 79.6 - - + +
22A ALA* 1.3 60.9 + - - +
24A ARG* 3.4 27.9 + - - +
25A GLU* 2.9 39.7 + - - +
109A ARG* 2.6 25.7 + - - +
203A GOL 2.8 28.8 + - - +
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Residues in contact with ALA 22 (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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9A ILE* 3.4 31.1 - - + +
11A VAL* 3.3 34.1 - - + -
18A ALA 3.1 8.1 + - - +
19A ILE 3.9 2.0 - - - +
21A GLN* 1.3 81.0 + - - +
23A THR* 1.3 65.3 + - - +
25A GLU 3.3 0.9 + - - -
26A LEU* 3.0 21.3 + - - +
88A ILE* 5.5 1.3 - - + -
109A ARG* 3.8 12.8 - - - +
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Residues in contact with THR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.6 0.2 - - - +
19A ILE* 2.8 26.9 + - - +
20A HIS 3.7 3.8 - - - -
22A ALA* 1.3 75.5 - - - +
24A ARG* 1.3 63.5 + - - +
26A LEU* 3.3 6.5 + - - +
27A LEU* 2.9 27.7 + - + +
47A PHE* 3.9 17.5 - - + -
58A PRO* 3.7 42.0 - - + +
61A ALA* 3.7 8.1 - - + -
88A ILE* 3.7 21.7 - - + +
90A VAL* 5.5 1.1 - - + -
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Residues in contact with ARG 24 (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 HIS* 3.0 35.4 + - - +
21A GLN* 3.6 19.9 - - - +
23A THR* 1.3 78.1 - - - +
25A GLU* 1.3 62.5 + - - +
27A LEU* 3.3 5.9 + - - +
28A LEU* 3.0 35.7 + - + +
61A ALA* 3.8 14.5 - - + +
64A GLN* 2.9 33.2 + - - +
65A ILE* 3.7 28.3 - - + -
203A GOL 2.6 43.2 + - - -
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Residues in contact with GLU 25 (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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9A ILE* 4.1 6.8 - - + +
21A GLN* 2.9 34.3 + - - +
22A ALA 3.6 5.4 - - - +
24A ARG* 1.3 76.6 - - - +
26A LEU* 1.3 62.6 + - - +
28A LEU* 3.9 2.5 - - - +
29A LYS* 3.0 64.6 + - + +
108A LEU* 3.9 10.3 - - + +
109A ARG* 2.9 22.1 + - - +
203A GOL 3.2 28.8 + - - +
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Residues in contact with LEU 26 (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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7A GLY* 3.7 6.3 - - - -
8A ALA* 3.5 38.6 - - - +
9A ILE* 3.8 22.9 - - + -
22A ALA 3.0 16.7 + - - +
23A THR* 3.7 4.3 - - - +
24A ARG 3.2 0.2 - - - -
25A GLU* 1.3 74.0 - - - +
27A LEU* 1.3 66.3 + - - +
29A LYS* 3.3 1.4 + - - -
30A MET* 2.9 35.4 + - + +
88A ILE* 3.9 7.4 - - + +
90A VAL* 3.6 26.0 - - + -
106A VAL* 3.7 25.6 - - + +
108A LEU* 4.0 9.8 - - + +
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Residues in contact with LEU 27 (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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23A THR* 2.9 37.8 + - + +
24A ARG* 3.7 3.8 - - - +
26A LEU* 1.3 76.0 - - - +
28A LEU* 1.3 63.9 + - - +
30A MET* 3.3 7.6 + - - +
31A LEU* 3.1 31.0 + - + +
45A VAL* 4.6 7.0 - - + -
47A PHE* 4.1 19.7 - - + -
61A ALA 4.5 1.3 - - - -
62A ALA* 3.8 36.1 - - + +
65A ILE* 4.1 15.0 - - + -
67A MET* 4.3 10.8 - - + -
90A VAL* 4.3 21.8 - - + -
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Residues in contact with LEU 28 (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 ARG* 3.0 25.1 + - + +
25A GLU* 3.9 3.8 - - - +
27A LEU* 1.3 76.6 - - - +
29A LYS* 1.3 57.9 + - + +
31A LEU* 3.3 6.0 + - + +
32A GLU* 2.9 29.6 + - - +
65A ILE* 4.0 30.1 - - + -
203A GOL 3.5 33.0 - - - +
301A MES 3.9 29.7 - - - +
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Residues in contact with LYS 29 (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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25A GLU* 3.0 48.7 + - + +
26A LEU 3.8 2.9 - - - +
28A LEU* 1.3 75.9 - - + +
30A MET* 1.3 60.7 + - - +
32A GLU* 3.7 16.7 - - - +
33A ALA* 2.8 33.4 + - - +
106A VAL* 3.9 14.0 - - + +
108A LEU* 3.4 33.7 - - + +
203A GOL 5.3 1.1 - - - -
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Residues in contact with MET 30 (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* 3.5 43.5 - - + +
6A ARG 3.6 15.3 - - - +
7A GLY* 3.7 14.6 - - - +
26A LEU* 2.9 30.0 + - + +
27A LEU* 3.3 9.8 + - - +
29A LYS* 1.3 76.5 - - - +
31A LEU* 1.3 63.0 + - + +
34A ASN* 2.9 31.9 + - - +
36A ILE* 4.8 1.7 - - - +
90A VAL* 3.7 29.6 - - + -
92A ALA* 4.3 6.1 - - + -
106A VAL* 3.9 26.2 - - + -
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Residues in contact with LEU 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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27A LEU* 3.1 23.4 + - + +
28A LEU* 3.5 12.3 - - + +
30A MET* 1.3 77.7 - - + +
32A GLU* 1.3 63.3 + - - +
34A ASN 3.3 1.7 + - - -
35A GLY 3.2 2.9 + - - -
36A ILE* 3.0 61.3 + - + +
39A TYR* 3.7 26.2 - - + +
42A LEU* 4.2 21.5 - - + -
65A ILE* 4.5 5.2 - - + -
67A MET* 5.2 2.9 - - + -
301A MES 3.6 29.8 - - - +
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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
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28A LEU 2.9 17.5 + - - +
29A LYS* 3.7 17.4 - - - +
31A LEU* 1.3 76.8 - - - +
33A ALA* 1.3 62.5 + - - +
35A GLY* 3.1 13.8 + - - +
301A MES 5.1 4.4 - - - -
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Residues in contact with ALA 33 (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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29A LYS 2.8 21.5 + - - +
30A MET 4.0 2.7 - - - +
32A GLU* 1.3 75.0 + - - +
34A ASN* 1.3 59.3 + - - +
35A GLY 3.4 0.6 + - - -
104A ARG* 3.5 35.0 - - + +
106A VAL* 3.9 16.8 - - + -
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Residues in contact with ASN 34 (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 16.0 - - - +
30A MET 2.9 23.8 + - - +
31A LEU 3.3 2.0 + - - -
32A GLU 3.1 0.4 - - - -
33A ALA* 1.3 79.4 - - - +
35A GLY* 1.3 64.9 + - - +
36A ILE* 3.2 12.4 + - + -
94A TRP* 3.6 39.3 - - + -
98A THR* 5.8 0.2 - - - +
102A ARG 4.4 1.2 - - - +
103A VAL* 3.6 8.1 - - - +
104A ARG* 2.7 50.0 + - - +
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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
------------------------------------------------------------
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