Contacts of the helix formed by residues 12 - 24 (chain A) in PDB entry 4R54
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 12 (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 3.8 2.6 + - - -
10A ALA 3.5 1.4 - - - -
11A THR* 1.3 81.6 - - - +
13A ALA* 1.3 66.9 + - - +
14A VAL 3.4 2.5 - - - -
15A GLY 3.8 2.0 - - - -
16A ALA* 3.0 22.9 + - - +
162A MET* 4.0 6.9 - - - +
403A NAP 3.2 36.3 + - - -
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Residues in contact with ALA 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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12A GLY* 1.3 73.8 - - - +
14A VAL* 1.3 63.9 + - - +
16A ALA* 3.6 8.4 + - - +
17A GLN* 3.6 17.5 + - - +
158A SER 4.2 12.1 - - - +
161A GLY 4.2 0.4 - - - -
162A MET* 3.6 28.5 - - + +
165A ILE* 4.5 5.4 - - + -
326A LEU* 4.0 15.6 - - + +
403A NAP 2.9 29.4 + - - +
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Residues in contact with VAL 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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13A ALA* 1.3 74.6 - - - +
15A GLY* 1.3 60.2 + - - +
17A GLN* 3.0 8.5 + - - +
18A MET* 2.8 42.1 + - + +
71A SER* 3.1 28.5 - - - +
94A ASN* 3.7 9.2 - - - +
326A LEU* 4.2 12.3 - - + -
330A ALA* 4.1 14.8 - - + -
331A ALA 4.5 2.5 - - - +
403A NAP 2.9 53.7 + - + +
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Residues in contact with GLY 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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7A VAL* 4.6 1.7 - - - +
9A GLY 3.3 26.1 + - - -
10A ALA* 3.4 13.1 - - - +
12A GLY 3.4 4.5 + - - -
13A ALA 3.3 0.8 - - - -
14A VAL* 1.3 79.6 - - - +
16A ALA* 1.3 61.3 + - - +
18A MET* 3.5 12.2 - - - +
19A ILE* 3.0 28.1 + - - +
71A SER* 5.0 0.2 + - - -
403A NAP 4.2 0.8 + - - -
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Residues in contact with ALA 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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10A ALA 3.7 5.2 + - - +
11A THR 5.8 0.7 - - - +
12A GLY 3.0 17.1 + - - +
13A ALA* 3.9 5.8 - - - +
14A VAL 3.3 0.2 - - - -
15A GLY* 1.3 75.5 - - - +
17A GLN* 1.3 69.3 + - - +
19A ILE* 3.5 10.5 + - - +
20A LYS* 3.2 25.8 + - - +
162A MET* 6.5 0.7 - - - -
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Residues in contact with GLN 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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13A ALA 3.6 11.7 + - - +
14A VAL 3.0 7.8 + - - +
16A ALA* 1.3 82.8 - - - +
18A MET* 1.3 61.1 + - - +
19A ILE 3.2 0.2 - - - -
20A LYS* 3.5 37.9 + - - +
21A MET* 2.8 35.0 + - - +
326A LEU* 3.8 31.7 - - + +
327A LEU* 3.7 19.3 - - + +
331A ALA* 3.5 15.0 - - + -
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Residues in contact with MET 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 VAL* 4.2 21.8 - - + -
14A VAL* 2.8 35.2 + - + +
15A GLY* 3.2 10.3 + - - +
17A GLN* 1.3 75.9 - - - +
19A ILE* 1.3 56.4 + - - +
21A MET* 3.4 3.2 + - - +
22A LEU* 2.9 37.4 + - - +
69A LEU* 3.9 30.1 - - + +
70A PHE 4.3 2.9 - - - +
71A SER* 3.7 23.8 - - - -
92A VAL 5.7 0.2 - - - +
94A ASN* 4.0 9.2 - - + -
331A ALA* 3.5 16.1 - - + +
334A SER* 3.7 30.1 - - - +
335A VAL* 4.3 1.7 - - - +
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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
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7A VAL* 4.9 5.8 - - + -
10A ALA* 3.6 26.0 - - + +
15A GLY 3.0 12.7 + - - +
16A ALA* 3.6 10.5 - - - +
17A GLN 3.2 0.2 - - - -
18A MET* 1.3 75.3 - - - +
20A LYS* 1.3 58.2 + - - +
22A LEU* 3.3 8.1 + - - +
23A GLU* 2.8 55.3 + - + +
34A TYR* 3.3 46.9 - - + +
45A LEU* 3.9 17.3 - - + -
46A LYS 3.8 5.6 - - - +
47A PHE* 4.3 1.7 - - + -
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Residues in contact with LYS 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 ALA 3.2 11.8 + - - +
17A GLN* 3.5 38.2 + - - +
19A ILE* 1.3 80.0 - - - +
21A MET* 1.3 70.9 + - + +
23A GLU* 3.2 16.2 + - - +
24A GLU* 3.0 49.1 + - - +
327A LEU* 5.9 0.2 - - + -
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Residues in contact with MET 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 GLN 2.8 23.5 + - - +
18A MET 3.9 0.4 - - - +
20A LYS* 1.3 87.7 - - + +
22A LEU* 1.3 56.7 + - - +
24A GLU* 3.3 13.3 + - - +
25A SER* 3.0 27.9 + - - -
298A GLY 6.0 0.4 - - - +
300A ARG* 3.5 43.5 + - - +
327A LEU* 3.9 26.2 - - + -
331A ALA* 4.0 3.1 - - + +
332A TRP* 3.8 36.9 - - + +
335A VAL* 3.7 27.3 - - + +
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Residues in contact with LEU 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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5A VAL* 4.3 12.6 - - + -
7A VAL* 3.5 33.4 - - + -
18A MET 2.9 21.0 + - - +
19A ILE* 3.7 5.2 - - - +
21A MET* 1.3 71.4 - - - +
23A GLU* 1.3 66.3 + - - +
24A GLU 3.0 1.6 - - - -
25A SER* 3.1 19.3 + - - +
27A LEU* 4.3 18.6 - - + -
29A ILE* 4.1 27.9 - - + +
32A ILE* 4.4 7.4 - - + -
47A PHE* 4.0 15.5 - - + -
48A LYS* 5.4 0.7 + - - -
69A LEU* 3.9 16.8 - - + -
335A VAL* 4.0 20.4 - - + -
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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 ILE* 2.8 38.1 + - - +
20A LYS* 3.5 21.1 + - - +
22A LEU* 1.3 77.0 - - - +
24A GLU* 1.3 62.8 + - + +
25A SER 3.4 2.6 + - - +
46A LYS* 4.1 3.3 - - - +
47A PHE* 3.7 24.5 - - + -
48A LYS* 2.9 62.8 + - + +
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Residues in contact with GLU 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 LYS* 3.0 36.2 + - + +
21A MET* 3.3 7.5 + - - +
22A LEU 3.0 0.2 - - - -
23A GLU* 1.3 80.1 - - + +
25A SER* 1.3 62.5 + - - +
26A THR* 5.3 2.1 - - - +
300A ARG* 2.8 44.5 + - - +
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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