Contacts of the strand formed by residues 51 - 59 (chain D) 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 LEU 51 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 6.3 2.9 - - + -
92A ALA* 4.8 6.7 - - + -
94B LEU* 4.5 10.5 - - + -
53C VAL* 5.0 3.6 - - + -
94C LEU* 3.5 33.2 - - + -
96C ALA* 4.1 22.4 - - + -
46D LEU* 4.4 4.3 - - + -
47D CYS* 3.2 4.6 - - - +
48D ASN* 2.8 47.0 + - - +
49D THR 3.5 2.0 + - - -
50D GLY* 1.3 79.5 - - - +
52D VAL* 1.3 70.8 + - - +
53D VAL* 3.8 18.6 - - + -
91D CYS* 4.2 1.2 - - - +
92D ALA* 3.4 29.4 - - + +
94D LEU* 4.9 0.9 - - + -
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 4.2 9.0 - - + -
45D THR* 4.1 14.4 - - + -
46D LEU 3.4 3.4 - - - +
47D CYS* 4.3 8.1 - - + +
51D LEU* 1.3 80.2 - - - +
53D VAL* 1.3 64.6 + - - +
54D LEU* 3.9 25.8 - - + -
70D ALA* 4.7 6.1 - - + -
74D ILE* 4.0 25.6 - - + -
91D CYS* 4.1 16.6 - - + -
92D ALA 2.9 6.5 + - - +
93D VAL* 3.3 18.6 - - + +
94D LEU 2.9 25.5 + - - -
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Residues in contact with VAL 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 4.3 18.7 - - + +
51C LEU* 4.8 6.3 - - + -
53C VAL* 4.3 20.4 - - + -
44D GLU 3.7 0.5 - - - +
45D THR* 3.2 7.1 - - - +
46D LEU* 2.6 55.5 + - + +
51D LEU* 3.8 26.0 - - + -
52D VAL* 1.3 77.5 - - - +
54D LEU* 1.3 70.9 + - - +
55D ALA* 4.8 2.0 - - + -
94D LEU* 3.5 27.1 - - + +
96D ALA* 5.5 0.2 - - + -
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.9 12.6 - - + -
28D ILE* 3.9 11.4 - - + -
44D GLU 3.5 2.7 - - - -
45D THR* 3.7 19.5 - - - +
52D VAL* 3.9 18.8 - - + -
53D VAL* 1.3 80.5 - - - +
55D ALA* 1.3 58.1 + - - +
66D TYR* 3.9 25.6 - - + +
70D ALA* 4.7 3.4 - - + -
93D VAL* 4.2 10.8 - - + -
94D LEU 2.9 12.0 + - - +
95D VAL* 4.0 14.6 - - + -
96D ALA* 2.7 33.8 + - - +
97D TYR* 3.5 30.9 + - + +
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Residues in contact with ALA 55 (chain D).
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* 4.3 17.7 - - + -
48C ASN* 4.0 16.6 - - - +
51C LEU* 5.8 0.4 - - + -
243C CYS* 3.8 19.5 - - - -
44D GLU* 2.8 34.6 + - - +
53D VAL* 4.2 3.1 - - + -
54D LEU* 1.3 74.8 - - - +
56D GLY* 1.3 60.4 + - - +
96D ALA* 4.3 4.9 - - + +
97D TYR* 3.2 21.8 - - - +
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Residues in contact with GLY 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ASN* 4.7 2.9 + - - +
243C CYS* 3.8 11.5 - - - +
42D ALA 3.3 8.7 - - - -
44D GLU* 4.5 0.9 - - - -
55D ALA* 1.3 80.1 - - - +
57D GLU* 1.3 77.7 + - - +
96D ALA 4.5 1.0 + - - -
97D TYR* 3.4 7.6 - - - +
98D ASP* 2.8 31.5 + - - +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ASN* 5.5 1.4 - - - +
241C GLY 4.4 10.2 - - - +
242C ASP* 3.3 28.7 - - - +
243C CYS* 2.8 30.1 + - - +
40D ARG 3.9 1.5 - - - +
41D VAL* 3.6 1.2 - - - -
42D ALA* 2.8 53.5 + - + +
44D GLU* 5.6 1.2 - - - +
56D GLY* 1.3 88.7 - - - +
58D ILE* 1.3 62.3 + - - +
98D ASP* 3.6 17.5 - - + +
273D LYS* 5.7 2.1 + - - +
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ILE* 4.8 2.0 - - + -
32D ILE* 4.1 22.2 - - + -
40D ARG 3.4 7.0 - - - +
41D VAL* 4.5 12.6 - - + -
43D ALA* 5.0 1.8 - - + -
57D GLU* 1.3 81.2 - - - +
59D THR* 1.3 64.3 + - - +
60D THR* 3.6 29.8 - - + -
66D TYR* 4.0 14.4 - - + +
97D TYR* 3.7 48.0 - - + -
98D ASP 3.0 8.2 + - - +
99D LYS* 3.1 13.1 - - + +
100D GLN* 3.0 24.8 + - - +
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Residues in contact with THR 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D SER* 3.5 3.3 - - - -
40D ARG* 2.8 48.2 + - + +
58D ILE* 1.3 73.2 + - - +
60D THR* 1.3 63.9 + - - +
100D GLN* 3.9 23.4 - - + +
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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