Contacts of the helix formed by residues 13 - 25 (chain A) in PDB entry 5VEY
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 TYR 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 3.3 35.2 - - + +
12A SER* 1.3 75.9 - - - +
14A SER* 1.3 53.1 + - - +
15A ILE 3.2 2.5 - - - -
16A TYR* 3.1 9.7 + + - -
17A VAL* 2.8 36.4 + - + +
38A MET 6.1 0.4 - - - -
39A ASN* 2.6 24.9 + - - +
42A VAL* 3.7 37.4 - - + +
43A ASN* 5.0 0.7 - - - -
114A PHE* 3.4 35.2 - + + -
115A PRO* 3.5 34.5 - - + +
118A ARG* 3.6 20.7 - - - +
119A VAL* 4.9 7.9 - - + +
122A LEU* 4.1 10.2 - - - +
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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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12A SER* 3.4 12.6 + - - -
13A TYR* 1.3 77.4 - - - +
15A ILE* 1.3 72.5 + - - +
17A VAL* 2.9 26.5 - - - +
18A TYR* 3.2 3.3 + - - +
35A MET* 2.9 36.2 - - - +
36A GLY 5.5 0.2 - - - -
39A ASN* 3.4 18.0 + - - +
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Residues in contact with ILE 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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12A SER* 4.6 12.3 + - - +
13A TYR* 3.2 0.4 - - - +
14A SER* 1.3 89.5 + - - +
16A TYR* 1.3 75.5 + - + +
18A TYR* 3.3 9.2 + - + +
19A LYS* 3.3 41.3 + - + +
35A MET* 4.8 1.8 - - + -
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Residues in contact with TYR 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 SER 3.5 25.4 - - - -
13A TYR* 3.1 17.0 + + - +
15A ILE* 1.3 85.6 - - + +
17A VAL* 1.3 65.4 + - - +
19A LYS* 3.2 32.4 + - + +
20A VAL* 3.3 16.8 + - - +
113A GLN* 2.9 40.4 - - + +
114A PHE* 3.9 20.9 - - + -
115A PRO* 3.7 25.9 - - + +
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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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13A TYR* 2.8 20.6 + - + +
14A SER* 2.9 32.3 - - - +
16A TYR* 1.3 69.4 - - - +
18A TYR* 1.3 66.7 + - - +
20A VAL* 3.1 9.6 + - - +
21A LEU* 3.0 21.1 + - + +
30A ILE* 4.5 5.2 - - + -
35A MET* 4.1 22.2 - - + +
38A MET* 4.3 20.2 - - + -
39A ASN* 5.3 0.2 - - - +
114A PHE* 4.8 2.9 - - + -
148A THR* 3.6 28.0 - - + -
152A LEU* 3.7 17.2 - - + +
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Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER 3.2 7.6 + - - +
15A ILE* 3.3 13.5 - - + +
16A TYR 3.2 0.2 - - - -
17A VAL* 1.3 83.2 - - - +
19A LYS* 1.3 62.8 + - + +
21A LEU* 3.2 12.7 + - + +
22A LYS* 3.1 22.1 + - + +
29A GLY* 5.4 3.4 - - - -
30A ILE* 3.4 43.4 + - + -
35A MET* 3.6 20.2 - - + -
166A ARG* 5.9 1.2 + - - -
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Residues in contact with LYS 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 ILE* 3.5 30.3 - - + +
16A TYR* 3.2 25.8 + - + +
17A VAL 3.2 0.4 - - - -
18A TYR* 1.3 78.2 - - + +
20A VAL* 1.3 60.3 + - + +
22A LYS* 3.1 15.5 + - - +
23A GLN* 2.8 26.3 + - - +
113A GLN* 4.0 27.9 - - + +
32B ASP 5.1 6.2 + - - -
33B LYS 5.0 8.5 - - - -
34B GLU 4.2 20.7 + - - +
35B GLY* 4.8 6.1 - - - +
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Residues in contact with VAL 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 TYR 3.5 14.4 - - - +
17A VAL* 3.1 12.7 + - - +
19A LYS* 1.3 78.3 - - + +
21A LEU* 1.3 57.8 + - - +
23A GLN 3.2 1.4 + - - -
24A VAL* 2.9 29.5 + - + +
113A GLN* 5.2 3.8 - - + -
114A PHE* 4.8 7.9 - - + -
145A GLU* 4.7 13.0 - - + +
148A THR* 4.7 3.8 - - + -
149A ALA* 3.7 33.2 - - + +
152A LEU* 3.9 9.2 - - + -
697C TYR* 3.1 39.7 - - + +
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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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17A VAL 3.0 11.3 + - - +
18A TYR* 3.2 16.1 + - + +
20A VAL* 1.3 77.4 - - - +
22A LYS* 1.3 57.3 + - - +
24A VAL* 3.3 13.3 - - + +
25A HIS 2.9 35.0 + - - +
28A THR* 3.1 39.3 - - - +
29A GLY* 3.3 26.0 - - - -
30A ILE* 3.4 18.4 - - + +
152A LEU* 4.2 19.9 - - + +
167A ILE* 3.7 18.8 - - + -
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Residues in contact with LYS 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 TYR* 3.1 13.6 + - + +
19A LYS* 3.1 14.4 + - - +
21A LEU* 1.3 78.4 - - - +
23A GLN* 1.3 56.9 + - + +
26A PRO* 3.0 51.1 - - + +
11B LYS* 3.2 36.3 - - - +
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Residues in contact with GLN 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 LYS* 2.8 22.5 + - - +
22A LYS* 1.3 74.1 - - + +
24A VAL* 1.3 64.0 + - - +
25A HIS 3.4 0.2 - - - -
26A PRO* 4.8 2.6 - - - +
113A GLN* 3.4 25.5 - - - +
697C TYR* 2.9 42.3 + - + -
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Residues in contact with VAL 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 VAL* 2.9 22.5 + - + +
21A LEU* 3.3 25.1 - - + +
23A GLN* 1.3 78.0 - - - +
25A HIS* 1.3 83.3 + - + +
26A PRO* 4.5 0.2 - - - -
149A ALA* 4.5 7.6 - - + +
152A LEU* 4.6 11.4 - - + -
153A GLU* 3.6 32.4 - - + +
697C TYR* 3.9 22.7 - - + -
699C LEU* 5.5 4.5 - - + -
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Residues in contact with HIS 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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21A LEU 2.9 16.2 + - - +
23A GLN 3.4 1.0 - - - -
24A VAL* 1.3 93.4 - - + +
26A PRO* 1.3 73.4 - - - +
27A ASP* 3.2 13.1 - - + +
28A THR* 3.0 44.8 + - + +
153A GLU* 4.9 15.7 - - - +
160A ARG* 5.2 15.0 - - - -
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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
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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