Contacts of the helix formed by residues 8 - 22 (chain A) in PDB entry 5CVE
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 ASP 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.4 2.6 - - - +
7A GLU* 1.3 86.4 - - + +
9A GLU* 1.3 59.7 + - - +
10A LYS* 3.1 18.2 + - - +
11A GLN* 3.0 52.8 + - + +
12A PHE* 2.9 26.7 + - - +
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Residues in contact with GLU 9 (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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6A ILE* 4.0 8.8 - - + +
7A GLU 4.3 0.2 - - - -
8A ASP* 1.3 73.4 + - - +
10A LYS* 1.3 65.7 + - + +
12A PHE* 3.1 8.9 + - + +
13A TYR* 3.1 38.5 + - + -
142A THR* 3.7 25.4 + - + +
145A HIS* 3.2 25.2 - - - -
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Residues in contact with LYS 10 (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 ASP* 3.1 11.7 + - - +
9A GLU* 1.3 80.2 - - + +
11A GLN* 1.3 59.4 + - + +
13A TYR* 3.4 5.7 + - - +
14A SER* 2.9 29.7 + - - -
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Residues in contact with GLN 11 (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 GLU* 6.1 0.9 - - - -
8A ASP* 3.0 40.7 + - + +
10A LYS* 1.3 74.4 - - + +
12A PHE* 1.3 61.0 + - - +
14A SER* 3.4 9.6 - - - +
15A LYS* 2.9 52.4 + - + +
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Residues in contact with PHE 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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6A ILE* 3.7 45.5 - - + -
8A ASP 2.9 13.4 + - - +
9A GLU 3.3 7.6 - - - +
11A GLN* 1.3 76.9 - - - +
13A TYR* 1.3 77.7 + + - +
15A LYS* 4.6 2.4 - - - +
16A ALA* 3.4 10.8 + - + +
139A GLY 3.6 22.0 - - - -
140A HIS 3.3 24.5 - - - -
141A LEU 4.5 2.2 - - - -
142A THR* 4.2 10.8 - - + -
176A LEU* 4.5 8.1 - - + -
181A SER* 2.7 57.5 + - - -
182A SER* 3.8 8.5 - - - -
183A VAL* 4.3 4.9 - - + -
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Residues in contact with TYR 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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9A GLU* 3.1 43.3 + - + +
10A LYS* 4.0 4.9 - - - +
12A PHE* 1.3 80.0 - + - +
14A SER* 1.3 65.3 + - - +
16A ALA* 3.3 6.8 + - + +
17A LYS* 3.0 22.9 + - - +
92A ILE* 5.7 3.0 - - + +
120A GLN* 3.5 35.8 - - + +
140A HIS 3.1 25.8 - - - -
141A LEU* 3.5 4.2 - - + +
142A THR* 3.1 26.3 + - + +
145A HIS* 2.6 41.7 + + - +
301A SAH 4.5 4.7 - - - -
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Residues in contact with SER 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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10A LYS 2.9 19.6 + - - -
11A GLN* 3.4 13.7 + - - +
13A TYR* 1.3 76.3 - - - +
15A LYS* 1.3 66.4 + - - +
17A LYS* 3.3 7.4 + - - +
18A THR* 3.1 27.5 + - - -
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Residues in contact with LYS 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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11A GLN* 2.9 41.9 + - + +
12A PHE* 4.6 1.1 - - - +
14A SER* 1.3 78.5 + - - +
16A ALA* 1.3 57.3 + - - +
18A THR* 3.4 7.5 + - - -
19A TYR* 2.9 28.9 + - - +
178A ASP* 3.3 30.2 + - - +
179A VAL 5.4 1.4 - - - +
180A ASP 5.3 0.2 - - - -
181A SER* 3.8 21.1 - - - +
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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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12A PHE* 3.4 17.1 + - + +
13A TYR* 3.3 9.6 + - + +
14A SER 3.3 0.4 - - - -
15A LYS* 1.3 76.3 - - - +
17A LYS* 1.3 65.6 + - - +
19A TYR* 3.3 1.3 + - - +
20A TRP* 3.1 31.6 + - + -
140A HIS* 3.5 33.4 - - + +
180A ASP 3.6 11.2 - - - -
181A SER* 3.6 4.9 - - - +
301A SAH 5.1 5.6 - - - +
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Residues in contact with LYS 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 TYR 3.0 16.5 + - - +
14A SER* 3.7 8.1 - - - +
16A ALA* 1.3 76.2 - - - +
18A THR* 1.3 63.6 + - - +
20A TRP* 3.3 5.5 + - - +
21A LYS* 3.2 41.8 + - + +
92A ILE* 4.4 45.8 - - + +
93A THR* 5.1 1.9 + - - +
301A SAH 6.3 0.2 - - - -
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A SER* 3.1 14.6 + - - -
15A LYS* 3.6 10.9 - - - +
16A ALA 3.3 0.2 - - - -
17A LYS* 1.3 74.2 - - - +
19A TYR* 1.3 66.6 + - - +
21A LYS* 3.3 36.5 + - - +
22A GLN* 3.5 25.3 - - - +
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Residues in contact with TYR 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 LYS 2.9 14.9 + - - +
16A ALA 3.5 8.5 - - - +
18A THR* 1.3 76.9 - - - +
20A TRP* 1.3 98.0 + + - +
22A GLN* 3.1 24.3 + - - +
23A ILE* 3.5 40.0 - - + +
32A GLY* 5.7 4.0 - - - -
179A VAL* 3.6 29.2 - - + +
180A ASP* 3.6 37.4 + - + +
1D PBE 5.3 6.1 - - + +
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Residues in contact with TRP 20 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA 3.1 23.8 + - - +
17A LYS* 3.3 3.8 + - - +
18A THR 3.3 0.2 - - - -
19A TYR* 1.3 97.8 - + - +
21A LYS* 1.3 65.0 + - - +
22A GLN 3.0 3.1 + - - -
23A ILE* 3.3 26.1 + - + +
29A GLY 3.8 23.6 - - - -
30A MET* 4.2 1.3 - - - -
92A ILE* 5.4 0.2 - - + -
93A THR* 3.6 22.3 - - - +
96A PHE* 3.3 41.0 - + + -
140A HIS* 2.9 29.5 + + - -
180A ASP* 5.1 0.9 - - - -
301A SAH 3.3 63.6 - + + +
1D PBE 3.7 25.6 - - + -
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Residues in contact with LYS 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 LYS* 3.2 27.7 + - + +
18A THR* 3.5 32.4 + - - +
19A TYR 3.2 0.4 - - - -
20A TRP* 1.3 76.4 - - - +
22A GLN* 1.3 62.8 + - + +
23A ILE 3.4 2.9 + - - +
93A THR* 4.8 14.8 - - + +
95A ASP* 5.7 0.9 - - - +
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Residues in contact with GLN 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 THR* 3.5 32.7 - - + +
19A TYR* 3.1 11.9 + - - +
20A TRP 3.0 1.2 - - - -
21A LYS* 1.3 84.3 - - + +
23A ILE* 1.3 65.0 + - + +
24A PRO* 3.9 5.5 - - - +
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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