Contacts of the strand formed by residues 69 - 77 (chain A) in PDB entry 5DO7
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 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 5.0 3.1 - - + +
44A SER* 2.3 32.5 + - - +
45A TYR* 2.8 39.6 + - + +
67A GLN* 3.1 4.2 + - - +
68A ILE* 1.3 88.5 - - + +
70A LYS* 1.3 54.9 - - - +
72A VAL* 4.5 7.0 - - + -
91A GLY* 3.9 17.5 - - - +
94A THR* 5.0 2.9 - - + -
95A LEU* 3.4 44.4 - - + +
98A ALA* 5.3 4.0 - - + -
266A LEU* 4.3 8.1 - - + -
269A GLY* 3.4 20.2 - - - +
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Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA 3.4 0.4 - - - -
44A SER* 3.2 1.3 - - - +
67A GLN* 3.7 28.9 - - - +
68A ILE 5.8 0.2 - - - -
69A LEU* 1.3 74.6 - - - +
71A ASP* 1.3 77.7 + - + +
72A VAL* 2.9 12.0 + - - +
268A PHE 5.8 0.2 - - - +
269A GLY 2.8 16.7 + - - +
270A GLU* 3.9 30.0 + - + +
271A LEU 4.3 6.6 + - - -
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Residues in contact with ASP 71 (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 HIS* 3.4 37.0 - - + +
43A ALA 2.8 16.7 + - - +
44A SER* 3.5 6.2 + - - -
70A LYS* 1.3 76.9 - - + +
72A VAL* 1.3 61.0 + - - +
73A SER* 4.0 4.0 + - - -
110A LEU* 3.6 21.8 - - - +
271A LEU* 4.6 6.6 - - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.2 5.5 - - + +
41A LEU 3.4 1.2 - - - -
42A HIS 2.8 16.6 + - - -
43A ALA* 2.8 26.4 + - + +
69A LEU* 4.5 12.1 - - + -
70A LYS 3.4 17.9 - - - +
71A ASP* 1.3 70.3 - - - +
73A SER* 1.3 79.2 + - - +
74A LEU* 3.4 23.8 - - + -
95A LEU* 4.4 20.9 - - + -
266A LEU* 4.7 7.4 - - + -
269A GLY 4.1 12.3 - - - +
271A LEU* 3.9 26.2 - - + +
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 2.9 16.8 - - - -
41A LEU* 4.0 7.4 - - - -
42A HIS* 3.0 25.5 + - - -
71A ASP 4.0 2.9 + - - -
72A VAL* 1.3 84.0 + - - +
74A LEU* 1.3 71.6 + - - +
271A LEU* 3.6 14.6 - - - +
274A CYS* 5.4 1.6 - - - +
338A THR* 4.8 11.3 - - - +
339A LEU* 5.2 12.9 - - - +
342A ILE* 5.7 0.7 - - - -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU 3.8 1.4 - - - +
39A GLY* 3.0 6.1 - - - -
40A ILE* 2.8 54.0 + - + +
72A VAL* 3.4 26.5 - - + -
73A SER* 1.3 90.3 - - - +
75A TYR* 1.3 60.0 + - - +
76A VAL* 5.3 2.5 - - + -
82A MET* 3.2 36.3 - - + -
84A ILE* 5.7 0.9 - - + -
264A ALA* 4.0 14.8 - - + -
266A LEU* 5.7 1.6 - - + -
271A LEU* 3.8 14.6 - - + -
274A CYS* 4.0 15.9 - - + -
338A THR* 4.9 6.1 - - - -
342A ILE* 3.5 4.8 - - - +
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Residues in contact with TYR 75 (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 SER* 4.8 1.4 - - - -
38A LEU 3.9 6.5 - - - -
39A GLY* 4.6 2.0 - - - -
74A LEU* 1.3 73.3 - - - +
76A VAL* 1.3 85.4 + - - +
77A GLU* 3.3 44.5 + - + +
80A GLN* 5.5 1.6 - - - -
82A MET* 5.4 0.2 - - - +
262A LYS* 3.1 30.0 + - - +
274A CYS* 5.2 0.5 - - - -
338A THR* 3.9 24.5 + - - +
341A ASN* 3.3 39.0 - - + -
342A ILE* 3.7 25.8 - - + -
345A MET* 3.4 44.0 - - + +
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Residues in contact with VAL 76 (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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36A HIS 3.3 1.2 - - - +
37A SER* 3.7 1.4 - - - -
38A LEU* 2.8 47.8 + - + +
74A LEU* 5.3 3.6 - - + -
75A TYR* 1.3 88.5 - - - +
77A GLU* 1.3 77.8 + - - +
80A GLN* 3.1 23.6 - - + +
81A ILE 5.3 0.2 - - - +
82A MET* 3.3 34.8 - - + -
244A ILE* 3.8 23.8 - - + -
245A VAL 5.4 0.7 - - - +
246A VAL* 5.6 2.7 - - + -
262A LYS* 4.9 2.5 - - + -
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Residues in contact with GLU 77 (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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35A PRO* 3.6 24.3 - - + +
36A HIS 2.5 16.7 - - - +
75A TYR* 3.3 39.1 + - + +
76A VAL* 1.3 73.8 - - - +
78A SER* 1.3 71.0 + - - +
80A GLN* 2.2 51.2 + - + +
244A ILE* 3.9 4.9 - - - +
341A ASN* 5.5 0.9 + - - -
345A MET* 5.1 4.2 - - - +
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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