Contacts of the helix formed by residues 11 - 24 (chain A) in PDB entry 1ML3
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 GLY 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLY* 3.4 6.1 + - - -
10A PHE* 1.3 82.8 - - - +
12A ARG* 1.3 65.2 + - - -
13A ILE* 3.2 4.7 - - - -
14A GLY 3.4 1.8 + - - +
15A ARG* 3.1 26.1 + - - -
38A ASP* 3.9 3.9 + - - -
110A SER 5.9 0.2 + - - -
206D VAL* 5.2 12.8 - - - -
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Residues in contact with ARG 12 (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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11A GLY* 1.3 72.0 - - - +
13A ILE* 1.3 73.0 + - + +
15A ARG* 3.5 27.2 + - - +
16A MET* 3.4 33.6 + - - +
53A ASP* 3.0 26.4 + - - -
54A THR* 4.8 0.6 + - - -
55A VAL* 3.3 32.3 - - - +
56A HIS* 4.2 0.4 - - - -
336A GLU* 2.8 31.8 + - - -
203D VAL* 4.8 14.4 - - + +
204D ASP* 3.1 45.2 + - - +
205D GLY* 5.7 1.1 - - - -
206D VAL* 6.0 0.4 - - - +
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Residues in contact with ILE 13 (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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11A GLY* 3.2 1.7 - - - -
12A ARG* 1.3 84.8 - - + +
14A GLY* 1.3 65.0 + - - +
16A MET* 3.5 5.5 + - - +
17A VAL* 3.2 29.3 + - + +
110A SER* 4.3 18.2 - - - +
134A SER* 4.2 26.7 - - - +
339A TYR* 5.4 9.0 - - + -
340A SER* 4.5 2.1 + - - +
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Residues in contact with GLY 14 (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 ILE* 4.3 11.2 - - - +
9A GLY 3.9 9.9 - - - -
10A PHE* 4.0 8.3 - - - -
11A GLY 3.4 8.0 + - - +
13A ILE* 1.3 80.3 - - - +
15A ARG* 1.3 62.5 + - - +
17A VAL* 3.1 9.4 + - - +
18A PHE* 2.9 22.0 + - - +
110A SER* 3.8 18.2 + - - -
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Residues in contact with ARG 15 (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 PHE* 3.7 39.0 + - + -
11A GLY* 3.1 28.9 + - - +
12A ARG* 3.5 44.3 - - - +
13A ILE 3.4 0.2 - - - -
14A GLY* 1.3 74.7 - - - +
16A MET* 1.3 54.9 + - + +
18A PHE* 3.0 3.5 + - - +
19A GLN* 2.6 49.0 + - + +
46A PHE 4.7 0.2 - - - -
49A GLN* 3.2 67.7 + - - +
50A MET* 3.9 12.8 - - + +
53A ASP* 5.4 0.6 + - - -
204D ASP* 4.0 11.1 + - - +
205D GLY* 5.5 0.4 - - - -
206D VAL* 6.1 1.0 - - - +
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Residues in contact with MET 16 (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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12A ARG* 3.4 24.5 + - - +
13A ILE* 3.8 7.2 - - - +
14A GLY 3.3 0.4 - - - -
15A ARG* 1.3 82.3 - - + +
17A VAL* 1.3 52.2 + - - +
19A GLN* 3.4 35.6 - - - +
20A ALA* 2.6 35.9 + - - +
53A ASP* 3.3 27.1 - - - +
56A HIS* 3.7 17.0 - - + -
336A GLU* 4.5 15.9 - - + +
337A TRP* 3.7 30.2 - - + -
340A SER* 2.9 23.2 - - - +
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Residues in contact with VAL 17 (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 ILE* 5.0 5.8 - - + -
13A ILE* 3.2 23.1 + - + +
14A GLY* 3.1 10.4 + - - +
16A MET* 1.3 75.3 - - - +
18A PHE* 1.3 58.8 + - - +
20A ALA* 3.3 3.5 - - - +
21A LEU* 3.0 28.4 + - + +
108A ILE* 4.3 22.0 - - + -
110A SER* 5.8 0.9 - - - -
134A SER* 5.2 3.1 - - - -
339A TYR* 5.9 1.1 - - + -
340A SER* 3.9 23.1 - - - +
343A VAL* 4.0 33.2 - - + -
344A VAL* 3.5 12.3 - - + +
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Residues in contact with PHE 18 (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 ILE* 4.0 10.3 - - + +
10A PHE* 3.9 19.7 - + + -
14A GLY 2.9 12.6 + - - +
15A ARG 3.4 7.4 - - - +
17A VAL* 1.3 75.3 - - - +
19A GLN* 1.3 64.1 + - + +
21A LEU* 3.3 9.4 + - + +
22A CYS* 3.0 52.1 + - - -
27A LEU* 4.1 21.1 - - + -
33A VAL* 4.3 22.0 - - + -
50A MET* 3.6 33.4 - - + -
59A PHE* 4.6 3.8 - + - -
78A LEU* 6.0 2.7 - - + -
80A VAL* 3.9 20.0 - - + -
85A ILE* 4.2 19.5 - - + -
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Residues in contact with GLN 19 (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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15A ARG* 2.6 37.2 + - + +
16A MET* 3.4 32.8 - - + +
18A PHE* 1.3 75.9 - - + +
20A ALA* 1.3 60.5 + - - +
22A CYS* 3.2 2.5 + - - +
23A GLU* 2.9 32.4 + - - +
49A GLN 4.5 2.6 - - - +
50A MET* 3.8 28.2 + - + +
53A ASP* 4.7 4.9 - - - +
56A HIS* 5.5 2.6 - - - +
59A PHE* 3.7 40.5 - - + +
337A TRP* 4.5 20.7 - - + -
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Residues in contact with ALA 20 (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 MET 2.6 22.1 + - - +
17A VAL 3.3 6.7 - - - +
19A GLN* 1.3 73.6 - - - +
21A LEU* 1.3 64.4 + - - +
22A CYS 3.1 1.2 + - - -
23A GLU* 3.2 6.0 + - - +
24A ASP* 3.1 20.1 + - - -
337A TRP* 5.7 2.2 - - - -
340A SER* 3.7 27.8 - - - +
341A HIS* 3.7 29.6 - - + +
344A VAL* 3.9 5.2 - - + -
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Residues in contact with LEU 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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5A VAL* 5.5 2.9 - - + -
7A ILE* 6.4 0.4 - - + -
17A VAL* 3.0 15.2 + - + +
18A PHE* 3.5 11.7 - - + +
20A ALA* 1.3 80.2 - - - +
22A CYS* 1.3 64.5 + - - +
24A ASP 3.7 0.9 + - - -
25A GLY 3.6 2.6 + - - -
26A LEU* 3.1 34.5 + - + +
27A LEU* 3.7 39.3 - - + +
31A ILE* 3.4 41.1 - - + -
33A VAL* 3.8 15.0 - - + -
344A VAL* 3.8 21.2 - - + +
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Residues in contact with CYS 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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18A PHE* 3.0 50.2 + - - +
19A GLN 3.5 7.6 - - - +
20A ALA 3.1 0.4 - - - -
21A LEU* 1.3 77.8 - - - +
23A GLU* 1.3 61.7 + - - +
25A GLY* 2.7 21.0 + - - -
27A LEU* 3.7 26.2 - - - -
59A PHE* 3.9 21.1 - - + -
61A TYR* 3.3 22.6 + - + -
80A VAL* 4.2 4.3 - - - -
81A ASN* 5.4 1.5 + - - +
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Residues in contact with GLU 23 (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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19A GLN 2.9 17.0 + - - +
20A ALA 3.2 0.9 + - - +
22A CYS* 1.3 74.4 - - - +
24A ASP* 1.3 67.7 + - - +
25A GLY* 3.1 1.2 + - - -
59A PHE* 5.5 1.5 - - + -
60A LYS* 5.8 11.9 - - + -
61A TYR* 4.0 17.5 + - + -
305A ASN* 3.8 16.9 + - - -
337A TRP* 2.9 36.2 + - + -
341A HIS* 3.2 30.5 + - + -
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Residues in contact with ASP 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 ALA 3.1 12.7 + - - +
21A LEU 4.0 0.2 - - - +
22A CYS 3.1 1.0 - - - -
23A GLU* 1.3 84.3 - - - +
25A GLY* 1.3 61.8 + - - +
26A LEU* 3.8 31.8 - - + +
305A ASN* 5.6 1.2 + - - -
341A HIS* 3.3 29.6 + - - +
344A VAL* 4.7 4.5 - - - +
345A ASP* 4.5 11.6 - - - +
348A ARG* 5.0 6.5 + - - +
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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