Contacts of the strand formed by residues 50 - 57 (chain A) in PDB entry 3E7O
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 ILE 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.9 6.1 - - - -
45A ASP* 2.8 31.8 + - - +
48A LEU* 3.9 33.2 - - + +
49A GLY* 1.3 84.9 - - - +
51A ASN* 1.3 64.2 + - - +
52A VAL* 4.1 17.7 - - + -
89A LEU* 4.6 9.2 - - + -
109A GLU* 6.2 1.6 - - + -
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Residues in contact with ASN 51 (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* 5.6 1.6 - - + -
43A ALA 3.2 11.4 - - - +
44A PHE* 4.0 20.8 - - - +
50A ILE* 1.3 82.1 - - - +
52A VAL* 1.3 61.4 + - - +
109A GLU* 5.6 0.2 - - - -
110A LEU* 3.6 35.6 + - + +
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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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26A TYR* 3.9 19.7 - - + -
42A ALA* 3.2 8.1 - - - +
43A ALA* 2.6 41.4 + - + +
45A ASP* 4.0 22.4 - - + +
50A ILE* 4.1 10.8 - - + -
51A ASN* 1.3 79.2 - - - +
53A ALA* 1.3 60.0 + - - +
54A VAL* 4.2 8.7 - - + -
89A LEU* 3.8 24.2 - - + -
107A VAL* 3.7 21.1 - - + -
108A MET 3.6 9.0 - - - +
109A GLU* 5.5 0.2 - - - -
110A LEU* 3.8 9.6 - - - +
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Residues in contact with ALA 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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1A 35F 3.7 40.8 - - + +
40A VAL* 4.1 9.2 - - + -
41A CYS 3.3 6.7 - - - +
52A VAL* 1.3 73.2 - - - +
54A VAL* 1.3 62.8 + - - +
55A LYS 4.0 0.2 - - - -
106A LEU 3.5 1.7 - - - +
107A VAL* 3.3 5.7 - - - +
108A MET* 2.9 41.5 + - + +
109A GLU 4.3 0.2 - - - +
110A LEU* 4.1 10.9 - - + +
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Residues in contact with VAL 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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20A PHE* 3.8 13.2 - - + -
22A VAL* 4.2 13.2 - - + -
26A TYR* 4.6 9.9 - - + -
29A LEU* 5.0 2.5 - - + -
39A ILE 3.6 2.1 - - - +
40A VAL* 3.3 4.0 - - - -
41A CYS* 2.6 42.7 + - + +
43A ALA* 3.8 28.3 - - + -
52A VAL* 4.2 9.9 - - + -
53A ALA* 1.3 76.3 - - - +
55A LYS* 1.3 61.2 + - - +
56A LYS 4.2 0.2 - - - -
92A PHE* 4.6 4.9 - - + -
105A TYR* 4.1 28.9 - - + -
106A LEU 3.5 4.5 - - - +
107A VAL* 4.5 11.0 - - + -
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Residues in contact with LYS 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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1A 35F 4.4 20.5 + - - +
37A GLN* 3.7 18.6 + - - +
38A GLY* 3.8 25.8 - - - -
39A ILE 3.5 3.4 - - - -
40A VAL* 4.0 15.9 - - + +
53A ALA 4.0 0.4 + - - -
54A VAL* 1.3 74.0 - - - +
56A LYS* 1.3 62.6 + - - +
57A LEU* 3.8 14.7 + - + +
73A GLU* 2.7 33.2 + - - +
104A VAL 3.7 0.7 - - - +
105A TYR* 3.2 5.9 - - - -
106A LEU* 2.7 45.6 + - + +
108A MET* 3.7 30.7 - - + -
169A ASP* 6.1 2.2 - - - +
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Residues in contact with LYS 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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18A SER* 4.3 10.9 + - - +
19A THR 2.9 25.5 + - - +
20A PHE* 3.9 21.4 - - + -
38A GLY* 3.3 0.9 - - - -
39A ILE* 3.1 32.9 + - + +
54A VAL 4.2 0.6 - - - -
55A LYS* 1.3 73.0 - - - +
57A LEU* 1.3 76.1 + - - +
58A SER* 3.2 4.3 + - - -
103A ASP* 3.9 25.1 + - + +
104A VAL 3.5 6.7 - - - +
105A TYR* 3.3 41.7 + - + +
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Residues in contact with LEU 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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37A GLN 3.4 14.4 - - - +
55A LYS* 3.8 8.2 + - + -
56A LYS* 1.3 81.2 - - - +
58A SER* 1.3 60.3 + - - +
59A ARG 3.1 8.0 + - - -
60A PRO* 3.7 19.9 - - + +
70A ALA* 3.9 33.2 - - + +
73A GLU* 3.4 24.0 - - - +
74A LEU* 6.1 1.8 - - + -
103A ASP* 5.3 2.6 - - - +
104A VAL* 2.9 49.1 + - + +
106A LEU* 3.8 21.8 - - + -
356A ILE* 6.3 0.4 - - + -
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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