Contacts of the strand formed by residues 52 - 62 (chain E) in PDB entry 1I5L
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 GLU 52 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48E ILE* 3.5 3.0 - - - +
49E GLN 2.9 33.3 + - - +
50E ASN 2.9 14.5 + - - +
51E GLY* 1.3 79.8 - - - +
53E VAL* 1.3 69.2 + - - +
54E VAL* 3.7 3.4 - - + +
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Residues in contact with VAL 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E GLU* 4.3 31.4 - - + +
47E GLU 3.5 9.0 - - - +
48E ILE* 4.5 12.6 - - + +
51E GLY 4.0 2.9 + - - +
52E GLU* 1.3 81.3 + - - +
54E VAL* 1.3 64.9 + - - +
55E ARG* 3.3 25.4 - - - +
56E LYS* 5.0 4.9 - - + -
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Residues in contact with VAL 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ARG* 5.4 6.5 - - - +
47E GLU* 2.9 22.9 + - + +
48E ILE 4.8 0.4 - - - -
49E GLN* 3.7 44.2 - - + +
52E GLU* 3.7 6.3 - - + +
53E VAL* 1.3 79.3 - - - +
55E ARG* 1.3 71.4 + - - +
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Residues in contact with ARG 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 4.2 25.1 - - - +
20D ARG* 5.1 0.4 - - - +
26D GLU* 2.9 39.0 + - - -
69D PHE* 4.8 14.6 - - - -
71D SER* 6.0 1.2 - - - -
27E PHE* 5.9 0.9 - - - -
45E ALA 4.2 0.2 - - - +
46E GLU* 3.4 2.4 - - - -
47E GLU* 2.9 58.9 + - + +
53E VAL* 3.3 11.8 - - - +
54E VAL* 1.3 83.9 + - - +
56E LYS* 1.3 60.0 + - - +
57E VAL* 3.9 26.7 - - + +
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Residues in contact with LYS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ALA 3.3 4.3 - - - +
46E GLU* 3.3 40.6 - - + -
53E VAL* 5.0 5.4 - - + -
55E ARG* 1.3 76.3 - - - +
57E VAL* 1.3 72.5 + - - +
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Residues in contact with VAL 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D PHE* 5.7 1.8 - - + -
71D SER* 3.7 24.9 - - - +
27E PHE* 4.2 8.1 - - + -
44E ASP* 3.6 2.6 - - - -
45E ALA* 2.7 54.6 + - + +
46E GLU* 5.4 0.2 - - - -
55E ARG* 3.9 28.0 - - - +
56E LYS* 1.3 85.8 - - - +
58E GLY* 1.3 61.7 + - - +
59E SER 3.1 2.8 + - - +
60E VAL* 3.6 25.8 - - + -
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Residues in contact with GLY 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D SER* 5.0 1.0 + - - -
72D PRO 5.5 3.2 + - - -
43E LEU* 3.7 5.2 - - - +
44E ASP* 3.1 22.0 + - - +
57E VAL* 1.3 72.3 - - - +
59E SER* 1.3 66.6 + - - +
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Residues in contact with SER 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 5.5 6.9 - - - +
71D SER* 3.0 24.3 + - - -
72D PRO* 3.5 25.2 + - - +
41E VAL* 5.5 2.7 - - - -
42E LEU 2.9 18.2 - - - -
43E LEU* 3.3 16.6 - - - +
44E ASP 4.5 0.2 - - - +
45E ALA 5.5 0.2 - - - +
57E VAL* 3.1 4.8 - - - +
58E GLY* 1.3 82.7 - - - +
60E VAL* 1.3 66.8 + - - +
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Residues in contact with VAL 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D PHE* 4.2 11.2 - - + -
70D VAL 3.6 4.9 - - - +
71D SER* 3.9 13.7 - - - -
72D PRO* 5.2 0.7 - - - -
27E PHE* 4.0 24.5 - - + -
40E LEU 3.8 0.3 - - - +
41E VAL* 3.2 7.5 - - - +
42E LEU* 2.9 60.7 + - + -
45E ALA* 4.4 4.3 - - + -
57E VAL* 3.6 18.8 - - + -
59E SER* 1.3 81.4 - - - +
61E VAL* 1.3 65.6 + - - +
62E ILE* 4.0 11.7 - - + -
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Residues in contact with VAL 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PRO* 4.2 23.8 - - + +
8D VAL* 3.8 30.5 - - + -
9D LEU* 4.8 13.5 - - + +
38D MET* 4.5 20.6 - - + +
69D PHE* 3.2 5.1 - - - -
70D VAL* 3.0 40.4 + - + +
72D PRO* 6.5 0.7 - - + -
40E LEU 3.3 7.6 - - - +
41E VAL* 4.0 13.0 - - + -
60E VAL* 1.3 78.4 - - - +
62E ILE* 1.3 65.0 + - - +
63E ARG 4.1 0.2 + - - -
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Residues in contact with ILE 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D MET* 5.6 0.4 - - - -
68D VAL 3.6 11.9 - - - +
69D PHE* 4.4 9.6 - - + -
19E VAL* 4.3 16.8 - - + -
21E LEU* 4.2 13.5 - - + -
27E PHE* 4.2 20.4 - - + -
39E ASN* 3.2 8.0 - - - +
40E LEU* 2.9 37.8 + - + +
42E LEU* 3.9 30.3 - - + -
60E VAL* 4.5 10.1 - - + -
61E VAL* 1.3 77.1 - - - +
63E ARG* 1.3 75.0 + - - +
66E THR* 4.2 2.5 - - + -
67E VAL* 4.1 16.6 - - + -
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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