Contacts of the strand formed by residues 40 - 48 (chain C) in PDB entry 3IML
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 ARG 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C TYR* 4.0 13.0 + - - +
39C SER* 1.3 77.6 + - - +
41C VAL* 1.3 62.0 + - - +
57C GLU 4.5 1.1 - - - -
58C ILE* 3.4 3.8 - - - -
59C THR* 2.8 53.9 + - + +
270C ASP* 3.3 2.6 + - - -
272C SER* 3.2 38.9 + - - -
273C LYS* 3.9 9.2 - - - +
342C LYS* 5.7 8.5 - - - +
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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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29C LEU* 3.8 33.7 - - + -
32C ILE* 3.8 39.9 - - + -
39C SER* 4.1 6.7 - - - -
40C ARG* 1.3 79.9 - - - +
42C ALA* 1.3 61.2 + - - +
43C ALA* 3.8 19.1 - - + +
57C GLU 3.6 3.6 - - - -
58C ILE* 4.5 7.6 - - + +
268C GLY 3.2 21.7 - - - +
269C LYS* 3.4 1.0 - - - -
270C ASP* 2.9 24.4 + - + +
273C LYS* 3.3 10.7 + - - +
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Residues in contact with ALA 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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41C VAL* 1.3 74.5 - - - +
43C ALA* 1.3 59.9 + - - +
44C GLU* 3.5 12.4 + - - +
56C GLY* 3.4 8.7 - - - -
57C GLU* 2.8 49.2 + - + +
268C GLY 3.2 6.3 - - - -
269C LYS* 4.6 8.1 - - + +
273C LYS* 4.5 11.7 - - - -
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Residues in contact with ALA 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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25C SER* 2.7 43.8 + - - +
28C ILE* 4.3 6.1 - - + -
41C VAL* 3.8 17.9 - - + -
42C ALA* 1.3 70.4 - - - +
44C GLU* 1.3 60.6 + - - +
45C THR* 5.6 0.2 - - - +
55C ALA 3.7 4.9 - - - -
58C ILE* 4.8 1.6 - - + -
97C TYR* 3.9 26.5 - - + +
267C SER 4.1 0.5 - - - +
268C GLY* 2.7 18.3 + - - +
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Residues in contact with GLU 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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25C SER* 3.9 0.7 - - - -
42C ALA* 3.8 16.9 - - - +
43C ALA* 1.3 74.5 - - - +
45C THR* 1.3 66.2 + - - +
53C VAL 3.8 0.3 - - - +
54C LEU* 3.6 4.5 - - - +
55C ALA 2.8 38.5 + - - +
57C GLU* 5.9 0.4 - - - +
97C TYR* 4.7 1.2 + - - -
246C THR* 3.8 9.2 - - - +
267C SER 4.8 1.2 - - - +
269C LYS* 5.3 2.3 - - - -
18D ASP* 5.6 1.4 - - - +
46D LEU* 5.0 4.0 - - + +
243D CYS* 4.3 21.0 - - + +
245D LEU* 3.9 27.3 - - + +
248D ARG* 2.6 47.9 + - - -
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Residues in contact with THR 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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21C ALA* 3.5 22.1 - - + +
24C ILE* 3.8 26.8 - - + +
25C SER* 2.8 27.5 + - - -
28C ILE* 5.2 0.9 - - - +
43C ALA* 4.9 0.5 - - - +
44C GLU* 1.3 78.2 + - - +
46C LEU* 1.3 66.5 + - - +
47C CYS* 4.8 1.3 - - - -
52C VAL* 4.1 6.1 - - + -
53C VAL 3.4 3.4 - - - +
54C LEU* 3.8 16.2 - - + +
97C TYR* 5.2 0.7 + - - -
245C LEU* 3.4 5.0 - - - +
246C THR* 2.8 40.4 + - - -
46D LEU* 5.1 2.2 - - - -
245D LEU* 4.4 2.3 - - - +
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Residues in contact with LEU 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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45C THR* 1.3 75.8 - - - +
47C CYS* 1.3 71.9 + - - +
48C ASN* 4.4 2.9 - - + +
51C LEU* 4.8 7.2 - - + -
52C VAL* 3.2 3.6 - - - +
53C VAL* 2.7 53.7 + - + +
243C CYS* 4.0 20.9 - - - -
244C GLY 3.3 9.2 - - - +
245C LEU* 4.3 18.8 - - + -
44D GLU* 5.0 4.3 - - + +
45D THR 5.1 0.2 - - - -
46D LEU* 4.1 38.5 - - + +
53D VAL* 4.3 13.9 - - + +
55D ALA* 4.3 14.1 - - + -
245D LEU* 5.8 0.2 - - + -
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Residues in contact with CYS 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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17C PRO 3.8 22.2 - - - -
20C VAL* 4.2 14.1 - - + -
21C ALA* 4.1 17.0 - - - -
24C ILE* 4.9 1.8 - - + -
45C THR* 4.8 2.7 - - + -
46C LEU* 1.3 79.4 - - - +
48C ASN* 1.3 62.0 + - - +
51C LEU 3.3 8.1 - - - +
52C VAL* 3.9 17.3 - - + -
74C ILE* 6.2 0.4 - - + -
239C PRO* 4.1 16.0 - - + +
242C ASP 4.0 1.6 - - - +
243C CYS* 3.5 0.5 - - - -
244C GLY* 2.8 41.7 + - - -
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Residues in contact with ASN 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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46C LEU* 4.4 1.5 - - - +
47C CYS* 1.3 75.6 - - - +
49C THR* 1.3 75.9 + - - +
50C GLY 3.8 1.7 + - - -
51C LEU* 2.9 42.5 + - - +
52C VAL* 5.6 0.5 - - - +
91C CYS* 5.6 0.3 - - - +
239C PRO* 3.4 22.8 - - - +
242C ASP 5.0 0.2 - - - -
243C CYS* 4.1 22.0 - - + +
55D ALA* 4.0 15.3 - - - +
56D GLY 4.7 2.4 + - - +
57D GLU* 5.5 1.6 - - - +
96D ALA* 3.2 31.0 + - - +
98D ASP* 5.5 2.0 - - - +
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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