Contacts of the strand formed by residues 40 - 49 (chain C) 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 LEU 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B PRO* 4.5 0.4 - - - -
9C LEU* 4.3 16.6 - - + -
19C VAL* 4.0 24.5 - - + -
31C LEU* 4.4 13.0 - - + -
33C GLY 3.6 5.6 - - - +
34C TYR* 3.8 16.4 - - + +
38C MET* 3.5 14.6 - - + +
39C ASN* 1.3 83.8 - - - +
41C VAL* 1.3 67.5 + - - +
42C LEU* 4.9 2.5 - - + -
60C VAL 3.6 0.4 - - - +
61C VAL* 3.2 8.1 - - - +
62C ILE* 2.8 45.7 + - + +
67C VAL* 4.3 11.2 - - + -
70C VAL* 3.8 27.6 - - + -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 4.5 1.8 - - + -
5B PRO* 3.6 37.0 - - + -
8B VAL* 3.7 30.3 - - + -
31C LEU* 3.9 0.7 - - - +
32C ASP* 3.0 37.8 + - + +
33C GLY* 3.1 25.1 + - - +
40C LEU* 1.3 77.6 - - - +
42C LEU* 1.3 74.7 + - - +
43C LEU* 5.7 1.1 - - + -
59C SER* 5.2 5.6 - - - -
60C VAL 3.2 9.9 - - - +
61C VAL* 4.6 3.1 - - + -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 3.9 17.7 - - + -
19C VAL* 3.9 15.5 - - + -
27C PHE* 3.8 31.0 - - + -
29C GLY* 4.6 6.5 - - - +
30C THR 3.4 4.9 - - - +
31C LEU* 3.9 25.1 - - + +
40C LEU* 4.9 3.6 - - + -
41C VAL* 1.3 85.5 - - - +
43C LEU* 1.3 63.7 + - - +
45C ALA* 4.2 12.8 - - + -
59C SER* 3.0 9.8 - - - -
60C VAL* 2.9 45.1 + - + -
62C ILE* 3.9 15.5 - - + -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ARG* 6.3 1.3 - - - +
29C GLY* 3.6 1.2 - - - -
30C THR* 3.0 39.8 + - + +
32C ASP* 3.8 30.5 - - + +
41C VAL* 5.7 1.3 - - + -
42C LEU* 1.3 74.6 - - - +
44C ASP* 1.3 82.5 + - - +
45C ALA 3.1 3.5 + - - -
58C GLY 3.4 6.1 - - - +
59C SER* 3.5 22.2 - - - -
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Residues in contact with ASP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG 4.0 0.5 - - - +
29C GLY* 3.9 6.6 - - - -
30C THR* 4.6 5.4 + - - +
43C LEU* 1.3 85.3 - - - +
45C ALA* 1.3 56.5 + - - +
46C GLU* 5.5 1.8 - - - +
57C VAL 3.6 4.9 - - - -
58C GLY* 2.6 22.1 + - - +
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 4.1 17.3 - - + -
28C ARG 2.9 20.4 - - - +
29C GLY* 3.5 10.5 - - - -
42C LEU* 4.2 14.1 - - + -
43C LEU 3.8 3.4 - - - +
44C ASP* 1.3 76.2 - - - +
46C GLU* 1.3 62.9 + - - +
56C LYS* 3.5 4.4 - - - +
57C VAL* 3.0 36.8 + - + +
59C SER* 6.1 0.2 - - - -
60C VAL* 4.7 4.7 - - + -
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLU 3.6 0.2 - - - +
27C PHE* 3.3 12.4 - - - -
28C ARG* 3.0 45.8 + - + +
44C ASP 5.5 1.1 - - - +
45C ALA* 1.3 80.3 - - - +
47C GLU* 1.3 63.0 + - - +
48C ILE* 3.9 8.8 + - + +
53C VAL* 3.7 30.0 - - + +
55C ARG 3.4 7.9 - - - +
56C LYS* 3.4 35.0 + - + -
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 3.7 10.0 + - - -
69B PHE* 4.1 16.5 - - - -
21C LEU* 5.6 1.0 - - - +
25C ARG* 2.5 48.5 + - + +
26C GLU 3.4 7.9 - - - +
27C PHE* 4.2 18.4 - - + -
46C GLU* 1.3 73.4 - - - +
48C ILE* 1.3 65.3 + - - +
53C VAL* 3.4 4.0 - - - +
54C VAL* 2.8 34.9 + - + +
55C ARG* 2.9 47.6 + - + +
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLY 4.6 0.5 - - - +
25C ARG* 3.4 6.1 - - - -
26C GLU* 2.9 49.2 + - + +
28C ARG* 3.2 42.8 - - + -
46C GLU* 3.9 17.3 - - + +
47C GLU* 1.3 82.8 - - - +
49C GLN* 1.3 59.7 + - - +
50C ASN 4.1 1.4 + - - -
51C GLY* 3.7 28.9 - - - +
52C GLU 3.3 14.6 - - - +
53C VAL* 4.6 6.7 - - + -
54C VAL* 4.7 0.9 - - - -
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Residues in contact with GLN 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLY 5.7 1.1 - - - -
25C ARG* 2.8 46.9 - - + +
48C ILE* 1.3 71.9 - - - +
50C ASN* 1.3 75.9 + - + +
51C GLY 3.1 2.2 + - - -
52C GLU* 3.1 20.7 + - - +
54C VAL* 3.9 16.1 - - + +
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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