Contacts of the helix formed by residues 15 - 30 (chain B) in PDB entry 5SVE
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 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B HIS 4.5 1.6 - - - +
14B PHE* 1.3 77.0 - - - +
16B ALA* 1.3 65.9 + - - +
17B ASP* 3.3 18.8 - - - +
18B GLU* 3.0 24.4 + - - +
19B ILE* 3.1 24.8 + - - +
84B LYS* 4.1 9.9 + - - -
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP* 1.3 74.8 - - - +
17B ASP* 1.3 58.9 + - - +
19B ILE* 3.4 10.5 + - - +
20B LYS* 3.0 26.4 + - - +
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP* 3.3 20.6 - - - +
16B ALA* 1.3 74.6 - - - +
18B GLU* 1.3 66.8 + - - +
20B LYS* 3.5 10.8 + - + +
21B ARG* 3.0 51.0 + - + +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 3.2 20.4 - - + -
15B ASP* 3.0 35.0 + - - +
16B ALA 3.2 0.6 - - - -
17B ASP* 1.3 91.9 + - - +
19B ILE* 1.3 60.0 + - - +
20B LYS 3.2 0.2 - - - -
21B ARG* 3.5 28.7 + - - +
22B LEU* 3.0 35.6 + - - +
84B LYS* 3.1 22.4 + - - -
169B VAL* 4.2 15.1 - - + +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B MET* 3.6 29.8 - - + -
12B SER* 4.5 2.5 - - - +
14B PHE* 3.7 25.8 - - + +
15B ASP 3.1 19.6 + - - +
16B ALA* 3.7 8.1 - - - +
18B GLU* 1.3 75.4 - - - +
20B LYS* 1.3 59.6 + - - +
22B LEU* 3.6 6.8 + - - +
23B GLY* 2.9 23.9 + - - -
71B PHE* 3.9 26.4 - - + -
75B ILE* 4.4 7.0 - - + -
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 3.0 16.8 + - - +
17B ASP* 3.6 10.5 - - - +
18B GLU 3.2 0.2 - - - -
19B ILE* 1.3 74.9 - - - +
21B ARG* 1.3 65.4 + - + +
23B GLY* 3.0 11.2 + - - -
24B LYS* 3.0 44.4 + - + +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASP* 3.0 51.4 + - + +
18B GLU* 3.5 25.2 + - - +
20B LYS* 1.3 76.2 - - + +
22B LEU* 1.3 61.8 + - - +
24B LYS* 3.4 10.0 + - - +
25B ARG* 3.2 21.7 + - - +
169B VAL* 2.9 43.1 + - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LEU* 3.7 31.6 - - + -
14B PHE* 3.7 35.2 - - + -
18B GLU 3.0 21.1 + - - +
19B ILE 3.8 0.7 - - - +
21B ARG* 1.3 77.3 - - - +
23B GLY* 1.3 57.7 + - - +
25B ARG* 3.4 5.5 + - + +
26B PHE* 2.9 28.1 + - - +
71B PHE* 4.4 1.6 - - - -
74B PHE* 3.8 11.7 - - + -
75B ILE* 3.7 31.0 - - + -
78B VAL* 4.6 7.2 - - + -
169B VAL* 4.0 26.9 - - + +
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE 2.9 12.4 + - - -
20B LYS* 3.0 6.0 + - - -
22B LEU* 1.3 78.9 - - - +
24B LYS* 1.3 57.6 + - - +
26B PHE* 3.2 4.9 + - - +
27B LYS* 3.1 26.3 + - - +
71B PHE* 3.4 23.5 - - - -
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS* 3.0 44.7 + - + +
21B ARG* 3.4 6.7 + - - +
23B GLY* 1.3 74.9 - - - +
25B ARG* 1.3 60.2 + - - +
27B LYS* 3.8 6.7 + - - +
28B LYS* 3.4 20.3 + - - +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ASN 4.0 5.3 + - - -
368A VAL 3.2 22.8 + - - +
369A LEU* 3.8 27.3 - - + +
370A ASN* 2.4 40.8 + - - +
21B ARG 3.2 16.5 + - - +
22B LEU* 3.7 8.5 - - + +
23B GLY 3.2 0.6 - - - -
24B LYS* 1.3 77.1 - - - +
26B PHE* 1.3 63.8 + - - +
28B LYS* 3.4 15.0 + - - +
29B LEU* 3.2 48.7 + - + +
45B LEU* 4.3 5.1 - - - +
74B PHE* 5.2 0.7 - - + -
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU 2.9 14.8 + - - +
23B GLY 3.2 9.4 + - - +
25B ARG* 1.3 77.4 - - - +
27B LYS* 1.3 61.7 + - + +
29B LEU* 3.2 6.9 + - - +
30B ASP* 3.0 29.0 + - + +
35B GLY* 3.5 27.4 - - - -
36B SER* 4.1 2.0 - - - -
37B LEU* 3.6 30.5 - - + +
69B VAL 3.6 7.4 - - - -
70B ASP 3.4 36.1 - - - -
71B PHE* 3.5 24.9 - + + -
74B PHE* 3.6 29.1 - + + -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY 3.1 15.0 + - - +
24B LYS* 4.0 8.3 - - - +
25B ARG 3.3 0.2 - - - -
26B PHE* 1.3 80.2 - - + +
28B LYS* 1.3 62.3 + - - +
30B ASP* 3.2 25.7 + - - +
33B ASN* 5.3 6.3 + - - +
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS 3.4 16.4 + - - +
25B ARG* 3.7 26.0 - - - +
26B PHE 3.2 0.6 - - - -
27B LYS* 1.3 79.7 - - - +
29B LEU* 1.3 62.8 + - - +
30B ASP 3.6 0.9 + - - -
31B LEU* 4.0 15.8 - - - +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A VAL* 3.3 34.1 - - + +
25B ARG* 3.2 44.9 + - - +
26B PHE* 3.2 1.8 + - - +
28B LYS* 1.3 76.3 - - - +
30B ASP* 1.3 59.7 + - - +
31B LEU* 3.0 17.9 + - - +
37B LEU* 3.6 35.3 - - + +
41B GLU* 4.0 15.8 - - - +
42B PHE* 5.5 3.4 - - + -
45B LEU* 4.4 22.2 - - + -
74B PHE* 4.6 10.3 - - + -
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Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 3.0 20.9 + - + +
27B LYS* 3.2 19.7 + - - +
28B LYS 4.5 0.8 - - - +
29B LEU* 1.3 72.7 - - - +
31B LEU* 1.3 64.6 + - - +
32B ASP* 3.0 4.7 - - - +
33B ASN* 3.2 18.7 + - - +
34B SER* 3.0 9.0 + - - -
35B GLY* 2.6 34.3 + - - -
36B SER 3.0 9.6 - - - +
37B LEU* 3.5 7.6 - - + +
41B GLU* 4.0 0.4 - - - -
203B CA 2.4 31.7 - - - -
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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