Contacts of the helix formed by residues 20 - 32 (chain I) in PDB entry 5DSV
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 VAL 20 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I SER 4.6 0.7 - - - +
11I ALA* 3.7 32.1 - - - +
13I THR 4.0 7.0 - - - +
14I PHE* 3.7 29.8 - - + +
19I ARG* 1.3 71.8 - - - +
21I PHE* 1.3 65.1 + - - +
22I GLN 4.6 0.2 - - - +
23I VAL* 3.0 36.3 + - + +
24I GLU* 3.5 13.6 + - - +
123I THR 4.3 3.1 - - - +
80J LEU* 4.3 11.2 - - + +
129J ARG* 4.0 20.6 - - - +
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Residues in contact with PHE 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I SER* 4.1 9.6 - - - -
3I ILE* 3.6 40.8 - - + -
7I TYR 4.1 10.3 + - - -
8I ASP* 3.5 22.7 - - + -
13I THR 4.3 0.4 + - - -
15I SER* 3.4 35.9 - - - -
19I ARG* 3.3 50.6 + - + -
20I VAL* 1.3 74.6 - - - +
22I GLN* 1.3 58.0 + - - +
24I GLU* 2.9 31.6 + - - +
25I TYR* 2.9 42.2 + + + -
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Residues in contact with GLN 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H SER 3.8 13.9 + - - -
13H THR* 3.9 3.0 - - - +
14H PHE* 2.6 62.2 + - - +
8I ASP* 3.2 24.4 + - - +
9I LEU 3.6 21.3 + - - -
10I SER 3.6 7.1 + - - +
11I ALA* 3.8 22.2 - - + +
20I VAL* 5.0 0.4 - - + -
21I PHE* 1.3 79.3 - - - +
23I VAL* 1.3 57.5 + - - +
25I TYR* 3.9 7.2 - - - +
26I ALA* 3.4 18.5 + - - +
129I ARG* 4.2 6.3 - - - +
130I PRO* 4.0 6.8 - - + +
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Residues in contact with VAL 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ALA* 5.3 0.4 - - + -
20I VAL* 3.0 31.1 + - + +
22I GLN* 1.3 75.6 - - - +
24I GLU* 1.3 66.9 + - + +
25I TYR 3.1 1.3 - - - -
26I ALA* 2.9 8.8 + - + +
27I MET* 2.9 30.5 + - + +
123I THR* 4.0 25.1 - - - +
130I PRO* 4.2 9.9 - - + -
153I PRO* 4.4 5.6 - - + +
154I SER* 3.6 39.5 - - - +
129J ARG* 5.5 0.4 - - - +
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Residues in contact with GLU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ARG* 2.5 55.8 + - - +
20I VAL 3.5 9.4 + - - +
21I PHE* 2.9 20.7 + - - +
23I VAL* 1.3 76.6 - - + +
25I TYR* 1.3 62.5 + - + +
27I MET* 3.1 29.5 + - + +
28I LYS* 3.0 32.8 + - - +
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Residues in contact with TYR 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H TYR* 4.5 1.1 - + - -
14H PHE* 4.0 6.5 - - + -
15H SER 3.5 16.4 - - - +
16H PRO* 3.4 47.5 - - + +
18H GLY* 3.5 9.7 - - - -
2I SER* 5.2 3.3 - - - -
3I ILE 3.4 11.6 + - - -
8I ASP* 3.0 49.4 + - + +
21I PHE* 2.9 35.1 + + + +
22I GLN* 3.9 20.0 - - - +
24I GLU* 1.3 78.3 - - + +
26I ALA* 1.3 61.2 + - - +
28I LYS* 3.0 29.9 + - - +
29I ALA 3.1 9.5 + - - -
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Residues in contact with ALA 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H PHE* 3.4 34.0 - - + -
22I GLN 3.4 10.1 + - - +
23I VAL* 2.9 12.0 + - - +
25I TYR* 1.3 74.4 - - - +
27I MET* 1.3 66.8 + - - +
29I ALA* 3.3 17.0 + - - +
30I VAL* 3.7 4.3 + - - +
130I PRO* 4.4 5.6 - - + -
131I PHE 3.6 16.2 - - - +
132I GLY* 4.0 2.8 - - - -
153I PRO* 3.9 14.8 - - + +
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Residues in contact with MET 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I VAL* 2.9 23.9 + - + +
24I GLU* 3.1 38.3 + - + +
26I ALA* 1.3 74.8 - - - +
28I LYS* 1.3 57.9 + - - +
30I VAL* 2.8 29.4 + - + +
31I GLU* 3.3 8.8 + - + +
152I ASP* 4.2 23.1 - - - +
153I PRO* 4.0 24.2 - - + -
154I SER* 4.8 5.4 - - - -
169I ARG* 5.2 9.2 + - - +
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Residues in contact with LYS 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H PRO* 3.4 27.0 + - - +
17H ASP* 4.3 11.0 - - - +
18H GLY* 4.2 2.5 - - - -
24I GLU* 3.0 16.3 + - - +
25I TYR* 3.0 25.1 + - - +
27I MET* 1.3 72.3 - - - +
29I ALA* 1.3 62.4 + - - +
30I VAL 3.3 0.2 - - - -
31I GLU* 3.6 21.7 + - + +
32I ASN* 3.5 30.2 + - - +
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Residues in contact with ALA 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H PHE* 4.0 18.4 - - + -
18H GLY* 3.4 24.2 - - - +
25I TYR 3.1 5.8 + - - +
26I ALA 3.3 12.1 - - - +
27I MET 3.2 0.2 - - - -
28I LYS* 1.3 76.0 - - - +
30I VAL* 1.3 62.8 + - - +
32I ASN* 3.8 4.7 + - - +
33I SER* 3.8 9.7 + - - -
79I GLY* 3.7 13.7 - - - -
80I LEU* 4.6 7.3 + - + +
132I GLY* 3.9 12.6 - - - +
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Residues in contact with VAL 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I ALA 3.9 8.5 - - - +
27I MET* 2.8 16.9 + - - +
29I ALA* 1.3 74.6 - - - +
31I GLU* 1.3 61.3 + - - +
33I SER* 3.0 22.2 + - - +
78I ALA* 3.8 24.0 - - + +
79I GLY* 3.8 5.8 - - - -
133I CYS* 3.8 12.1 - - - -
134I SER* 3.4 36.8 - - - +
153I PRO* 4.1 6.5 - - + -
165I ILE* 4.6 0.4 - - + -
166I GLY* 3.5 8.2 - - - +
169I ARG* 3.4 25.6 - - - +
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Residues in contact with GLU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I MET* 3.8 5.4 - - - +
28I LYS* 3.6 34.0 + - + +
29I ALA 3.4 0.4 - - - -
30I VAL* 1.3 76.1 - - - +
32I ASN* 1.3 65.4 + - - +
33I SER 3.2 10.0 - - - +
166I GLY 3.6 17.2 - - - +
167I LYS* 3.2 23.8 - - - +
169I ARG* 4.0 25.4 + - - +
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Residues in contact with ASN 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ASP* 2.9 30.2 + - - +
18H GLY 5.0 4.0 + - - +
19H ARG* 5.2 6.3 - - - +
28I LYS* 3.5 13.5 + - - +
29I ALA* 3.8 5.8 + - - +
30I VAL 3.3 0.6 - - - -
31I GLU* 1.3 79.8 - - - +
33I SER* 1.3 59.1 + - - +
167I LYS* 4.0 17.3 + - - +
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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