Contacts of the strand formed by residues 13 - 22 (chain A) in PDB entry 5EPJ
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 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ALA* 1.3 75.8 - - - +
14A GLU* 1.4 66.6 + - - +
15A SER* 3.5 29.4 - - - +
16A ILE* 5.1 3.6 - - + -
30A VAL* 3.9 9.4 - - + -
31A LYS 3.9 5.6 - - - +
32A TRP* 3.8 9.2 - - + +
33A LYS* 4.0 11.4 + - - +
48A ILE* 5.9 1.1 - - + -
53A LEU* 4.1 19.1 - - + -
1B 5R0 2.9 30.0 + - - +
2B PHE 3.6 5.4 - - - +
3B ALA* 3.6 39.7 - - + +
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Residues in contact with GLU 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 VAL* 1.4 75.2 - - - +
15A SER* 1.3 69.1 + - - +
17A ARG* 5.6 3.3 + - - -
31A LYS* 2.6 58.0 + - + +
33A LYS* 3.5 32.1 - - + +
34A GLY 4.9 1.2 + - - -
53A LEU* 4.7 5.4 - - - +
1B 5R0 5.5 1.7 - - - -
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Residues in contact with SER 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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13A VAL* 3.5 13.1 - - - +
14A GLU* 1.3 89.0 + - - +
16A ILE* 1.3 63.7 + - - +
17A ARG* 3.2 24.6 - - - -
30A VAL* 3.8 0.5 - - - -
31A LYS* 2.9 31.6 + - - +
53A LEU* 4.8 5.6 - - - -
56A ALA* 6.4 2.5 - - - -
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Residues in contact with ILE 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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13A VAL* 4.6 4.0 - - + +
15A SER* 1.3 83.5 + - - +
17A ARG* 1.3 64.8 + - - +
18A LYS 3.8 10.1 - - - +
28A TYR* 3.7 30.5 - - + -
29A LEU 3.4 8.1 - - - +
30A VAL* 4.5 9.4 - - + -
48A ILE* 3.9 23.3 - - + -
53A LEU* 3.8 29.3 + - + +
54A VAL* 3.6 30.3 - - + +
57A TYR* 3.6 28.9 - - + +
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Residues in contact with ARG 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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14A GLU* 5.6 2.9 + - - -
15A SER* 3.2 21.1 - - - +
16A ILE* 1.3 76.5 - - - +
18A LYS* 1.3 65.1 + - - +
29A LEU* 2.8 24.4 + - + +
31A LYS* 3.7 36.1 - - + +
37A PRO* 5.3 4.8 - - - +
40A SER* 6.4 0.2 - - - -
57A TYR* 3.6 12.1 - - - -
109A UNX 3.4 26.3 - - - -
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Residues in contact with LYS 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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16A ILE* 3.7 5.2 - - - +
17A ARG* 1.3 79.9 - - - +
19A LYS* 1.3 64.9 + - - +
28A TYR* 3.4 4.3 - - - -
29A LEU* 2.8 39.2 + - + -
42A TRP* 3.7 28.7 - - + -
57A TYR* 3.7 12.6 - - - -
107A UNX 3.0 20.5 - - - -
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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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18A LYS* 1.3 86.5 + - - +
20A ARG* 1.3 68.1 + - - +
21A VAL* 5.9 0.9 - - + -
26A VAL* 3.6 35.3 - - + +
27A GLU 3.3 5.4 - - - -
28A TYR* 3.6 19.3 + - + +
42A TRP* 3.8 3.9 - - - -
57A TYR* 3.4 21.8 + - + +
58A GLU* 2.8 29.9 + - - -
107A UNX 4.1 6.6 - - - -
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Residues in contact with ARG 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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19A LYS* 1.3 77.4 - - - +
21A VAL* 1.3 69.6 + - - +
22A ARG* 3.6 18.5 - - - +
26A VAL* 3.4 7.1 - - - +
27A GLU* 2.8 60.4 + - + +
42A TRP* 3.4 62.6 - - + +
101A UNX 3.7 24.6 - - - -
108A UNX 3.5 13.0 - - - -
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Residues in contact with VAL 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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19A LYS* 5.9 1.6 - - + -
20A ARG* 1.3 79.3 - - - +
22A ARG* 1.3 63.2 + - - +
24A GLY* 3.7 35.4 - - - +
25A LYS 3.3 3.6 - - - +
26A VAL* 4.3 18.2 - - + -
101A UNX 4.0 8.8 - - - -
108A UNX 3.1 15.7 - - - -
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Residues in contact with ARG 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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20A ARG* 3.6 24.4 - - - +
21A VAL* 1.3 74.8 - - - +
23A LYS* 1.3 91.3 + - + +
24A GLY 3.2 0.2 - - - -
25A LYS* 3.0 21.3 + - - +
27A GLU* 2.8 44.3 + - - +
101A UNX 3.9 16.8 - - - -
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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