Contacts of the helix formed by residues 82 - 92 (chain D) in PDB entry 5M64
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 82 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D LYS* 3.4 36.3 - - - +
80D THR* 3.1 24.5 - - - +
81D ASN* 1.3 78.9 - - - +
83D SER* 1.3 67.9 + - - +
84D SER 3.3 1.8 - - - -
85D SER* 3.2 15.7 + - - +
86D ILE* 3.1 24.5 + - - +
63G LYS* 5.6 2.9 - - + -
67G ASN* 3.9 41.1 - - + +
70G VAL* 6.5 0.2 - - + -
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D THR* 3.2 17.0 + - - -
82D LEU* 1.3 80.7 - - - +
84D SER* 1.3 68.4 + - - +
86D ILE* 3.1 17.7 + - - +
87D SER* 3.0 19.4 + - - -
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Residues in contact with SER 84 (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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80D THR 4.8 1.5 + - - -
81D ASN* 5.1 7.8 - - - -
82D LEU* 3.3 1.0 - - - +
83D SER* 1.3 78.2 + - - +
85D SER* 1.3 64.2 + - - +
87D SER* 2.4 30.0 + - - -
88D GLN* 3.0 16.2 + - - +
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ASN 3.9 5.4 + - - -
82D LEU* 3.2 25.6 + - - +
84D SER* 1.3 77.1 - - - +
86D ILE* 1.3 60.0 + - - +
88D GLN* 3.2 20.8 + - - +
89D LEU* 2.9 39.4 + - - +
67G ASN 5.1 1.2 + - - -
70G VAL* 4.1 24.2 + - - +
71G MET* 4.6 2.9 - - - +
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Residues in contact with ILE 86 (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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44D ILE* 4.5 21.3 - - + +
47D LYS* 3.3 42.2 - - + +
48D GLU* 6.4 1.1 - - + -
82D LEU 3.1 13.8 + - - +
83D SER* 3.1 15.2 + - - +
85D SER* 1.3 75.3 - - - +
87D SER* 1.3 61.8 - - - +
89D LEU* 3.2 8.5 + - + +
90D LYS* 3.0 28.3 + - + +
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Residues in contact with SER 87 (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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83D SER 3.0 11.5 + - - -
84D SER* 2.4 32.4 + - - -
86D ILE* 1.3 78.1 - - - +
88D GLN* 1.3 60.4 + - - +
90D LYS* 3.1 21.8 - - - +
91D ARG* 2.9 40.5 + - - +
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Residues in contact with GLN 88 (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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84D SER* 3.3 9.2 + - - +
85D SER* 3.2 33.4 + - - +
87D SER* 1.3 79.1 + - - +
89D LEU* 1.3 61.4 + - + +
91D ARG* 3.7 12.1 - - - +
92D ILE* 3.1 33.4 + - - +
71G MET* 3.3 38.3 - - + +
151G ASP 5.6 1.3 - - - +
152G ALA* 4.9 23.0 - - + +
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Residues in contact with LEU 89 (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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40D LEU* 4.5 13.1 - - + +
43D PHE* 3.6 37.7 - - + -
44D ILE* 3.8 22.4 - - + -
85D SER* 2.9 29.1 + - - +
86D ILE* 3.2 7.6 + - + +
88D GLN* 1.3 77.1 - - + +
90D LYS* 1.3 59.5 + - - +
92D ILE* 3.1 32.0 - - + +
93D GLN* 3.2 18.3 + - - +
71G MET* 3.7 33.9 - - + -
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Residues in contact with LYS 90 (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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44D ILE* 5.3 5.7 - - + +
86D ILE* 3.0 19.7 + - + +
87D SER* 3.1 28.9 - - - +
89D LEU* 1.3 75.0 - - - +
91D ARG* 1.3 84.5 + - + +
93D GLN* 3.6 9.9 - - + +
94D ARG* 3.2 24.7 + - + +
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Residues in contact with ARG 91 (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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87D SER* 2.9 33.5 + - - +
88D GLN* 3.8 11.4 - - - +
89D LEU 3.3 0.2 - - - -
90D LYS* 1.3 100.5 - - - +
92D ILE* 1.3 56.5 + - - +
94D ARG* 3.2 22.1 - - + +
95D ASP* 3.4 2.6 - - - +
151G ASP* 3.0 48.1 + - - +
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Residues in contact with ILE 92 (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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36D VAL* 6.1 0.2 - - - +
40D LEU* 3.8 24.2 - - + +
88D GLN 3.1 15.8 + - - +
89D LEU* 3.1 29.6 - - + +
91D ARG* 1.3 75.2 - - - +
93D GLN* 1.3 62.7 + - - +
94D ARG 3.5 0.2 - - - -
95D ASP* 3.4 19.0 + - - +
96D PHE* 4.2 13.4 - - + -
71G MET* 5.9 0.4 - - + -
82G LEU* 5.0 21.1 - - + +
150G HIS* 3.3 28.9 - - + +
151G ASP* 4.3 0.7 - - - +
152G ALA* 3.6 19.1 - - + -
153G PHE* 6.4 0.2 - - + -
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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