Contacts of the strand formed by residues 51 - 59 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 5.1 5.2 - - + -
47A CYS* 3.1 5.4 - - - +
48A ASN* 2.8 46.5 + - + +
49A THR 3.5 3.2 + - - -
50A GLY* 1.3 78.9 - - - +
52A VAL* 1.3 73.2 + - - +
53A VAL* 4.0 18.4 - - + -
91A CYS* 4.6 3.7 - - - +
92A ALA* 3.3 18.2 - - + +
94A LEU* 4.8 6.5 - - + +
53B VAL* 5.2 1.6 - - + -
94B LEU* 4.0 25.1 - - + -
96B ALA* 3.8 29.2 - - + -
94C LEU* 4.9 3.6 - - + -
51D LEU* 6.3 2.7 - - + -
92D ALA* 4.7 8.7 - - + -
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Residues in contact with VAL 52 (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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24A ILE* 4.6 6.3 - - + -
45A THR* 4.1 6.7 - - + -
46A LEU 3.4 6.1 - - - +
47A CYS* 3.8 13.9 - - + -
51A LEU* 1.3 79.1 - - - +
53A VAL* 1.3 65.4 + - - +
54A LEU* 3.5 32.8 - - + -
70A ALA* 4.8 5.4 - - + -
74A ILE* 4.1 26.0 - - + -
91A CYS* 4.4 10.3 - - - -
92A ALA 2.9 8.5 + - - +
93A VAL* 3.3 18.5 - - + +
94A LEU 2.8 25.5 + - - -
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Residues in contact with VAL 53 (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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44A GLU 3.7 0.7 - - - +
45A THR* 3.2 8.7 - - - +
46A LEU* 2.6 55.1 + - + +
51A LEU* 4.0 22.4 - - + -
52A VAL* 1.3 76.6 - - - +
54A LEU* 1.3 70.7 + - - +
55A ALA* 4.8 2.5 - - + -
94A LEU* 3.5 28.9 - - + +
96A ALA* 5.5 0.4 - - + -
46B LEU* 4.4 16.7 - - + +
51B LEU* 4.9 2.5 - - + -
53B VAL* 4.3 25.1 - - + -
94B LEU* 4.6 0.4 - - + -
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Residues in contact with LEU 54 (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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24A ILE* 3.8 12.8 - - + -
28A ILE* 3.9 20.9 - - + -
44A GLU 3.5 2.9 - - - -
45A THR* 3.7 20.9 - - + +
52A VAL* 3.5 25.8 - - + -
53A VAL* 1.3 77.1 - - - +
55A ALA* 1.3 62.4 + - - +
66A TYR* 4.1 20.0 - - + +
70A ALA* 4.7 2.5 - - + -
93A VAL* 4.1 18.4 - - + -
94A LEU 2.9 8.8 + - - +
95A VAL* 4.1 13.7 - - + -
96A ALA* 2.8 29.5 + - - +
97A TYR* 3.6 19.7 + - + +
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Residues in contact with ALA 55 (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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44A GLU* 2.8 34.9 + - + +
53A VAL* 4.8 2.5 - - + -
54A LEU* 1.3 75.2 - - - +
56A GLY* 1.3 59.5 + - - +
96A ALA* 4.0 15.0 - - + +
97A TYR* 3.3 16.3 - - - -
46B LEU* 4.3 20.4 - - + -
48B ASN* 4.2 8.3 - - - +
51B LEU* 5.9 0.2 - - + -
243B CYS* 3.9 19.5 - - - -
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Residues in contact with GLY 56 (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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42A ALA 3.4 11.2 - - - -
44A GLU* 4.6 1.6 - - - -
55A ALA* 1.3 78.8 - - - +
57A GLU* 1.3 76.5 + - - +
96A ALA 4.3 1.4 + - - -
97A TYR* 3.3 9.5 - - - +
98A ASP* 2.7 31.2 + - - -
48B ASN* 4.6 1.6 + - - -
243B CYS* 4.1 9.3 - - - +
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Residues in contact with GLU 57 (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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40A ARG 4.0 0.6 - - - +
41A VAL* 3.7 0.7 - - - -
42A ALA* 2.9 45.6 + - + +
44A GLU* 5.6 1.4 - - - +
56A GLY* 1.3 88.7 - - - +
58A ILE* 1.3 64.6 + - - +
98A ASP* 3.5 25.1 - - + +
100A GLN* 5.4 2.7 - - - +
48B ASN* 4.6 4.0 - - - +
241B GLY 4.6 5.5 - - - +
242B ASP* 3.4 32.3 + - - +
243B CYS* 3.2 27.0 + - - +
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Residues in contact with ILE 58 (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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28A ILE* 5.0 0.7 - - + -
32A ILE* 4.1 19.7 - - + -
40A ARG 3.2 9.0 - - - +
41A VAL* 4.3 15.0 - - + -
42A ALA 4.9 0.2 - - - +
43A ALA* 5.1 0.7 - - + -
57A GLU* 1.3 79.9 - - - +
59A THR* 1.3 65.0 + - - +
60A THR* 3.7 27.8 - - + -
66A TYR* 3.8 16.8 - - + +
97A TYR* 3.6 48.9 - - + -
98A ASP 3.0 10.0 + - - +
99A LYS* 3.3 10.1 - - + -
100A GLN* 3.1 27.6 + - - +
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Residues in contact with THR 59 (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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39A SER* 3.5 2.6 - - - -
40A ARG* 2.7 51.8 + - + +
58A ILE* 1.3 73.0 - - - +
60A THR* 1.3 65.1 + - - +
100A GLN* 3.2 27.8 + - + +
101A SER 4.2 1.6 - - - +
102A PRO* 3.8 32.3 - - + -
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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