Contacts of the helix formed by residues 77 - 87 (chain H) in PDB entry 6ALG
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 ASP 77 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69H SER 4.6 13.3 - - - +
70H THR* 4.4 14.7 + - - +
71H LYS 5.3 2.9 + - - +
74H VAL 5.0 2.4 - - - +
75H GLN 3.7 10.5 - - - +
76H GLU* 1.3 78.4 - - - +
78H ILE* 1.3 63.7 + - - +
79H LEU* 3.2 13.2 - - + +
80H GLU* 2.9 14.8 + - + +
81H ILE* 2.8 26.0 + - - +
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Residues in contact with ILE 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H ILE* 4.7 9.6 - - + -
64H VAL* 3.7 31.9 - - + -
66H HIS 4.9 2.2 - - - +
67H GLU 4.4 13.5 - - - +
69H SER* 3.7 21.8 + - - -
70H THR* 4.0 14.8 - - - +
71H LYS* 4.4 16.8 - - + -
77H ASP* 1.3 72.6 - - - +
79H LEU* 1.3 65.1 + - - +
81H ILE* 3.3 26.5 + - + +
82H LEU* 3.5 14.1 - - + +
171H LEU* 3.7 28.9 - - + -
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Residues in contact with LEU 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H GLU* 4.5 10.1 + - + +
68H TYR* 4.3 31.4 - - + -
69H SER 5.5 2.3 + - - +
77H ASP* 4.0 8.9 - - + +
78H ILE* 1.3 78.1 - - - +
80H GLU* 1.3 58.0 + - - +
82H LEU* 4.3 9.8 + - + +
83H LEU* 3.6 17.7 - - - +
526J VAL* 4.1 26.2 - - + +
549J LYS* 4.5 24.0 - - + -
569J LEU* 5.2 4.6 - - + +
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Residues in contact with GLU 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H GLN 4.8 0.3 - - - +
76H GLU* 3.4 39.7 - - + +
77H ASP* 2.9 17.8 + - + +
79H LEU* 1.3 79.2 - - - +
81H ILE* 1.3 61.1 + - - +
82H LEU 3.3 3.2 + - - -
83H LEU* 3.6 10.8 + - - +
84H ASN* 3.7 3.2 - - - +
551J ARG* 3.3 31.9 + - - +
568J SER* 6.0 1.0 - - - -
569J LEU* 4.2 25.8 - - + +
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Residues in contact with ILE 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H ILE* 5.7 4.0 - - + -
74H VAL* 5.1 6.3 - - + -
76H GLU* 5.1 5.2 - - + +
77H ASP 2.8 10.7 + - - +
78H ILE* 3.3 29.2 - - + +
80H GLU* 1.3 78.6 - - - +
82H LEU* 1.3 75.8 + - + +
84H ASN* 3.3 9.9 + - - +
85H LEU* 3.3 23.3 + - + +
130H ILE* 3.6 24.7 - - + +
131H CYS* 3.7 26.7 - - + -
140H ILE* 5.5 3.8 - - + -
142H MET* 4.1 26.5 - - + -
171H LEU* 6.0 0.2 - - + -
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Residues in contact with LEU 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H VAL* 4.5 4.7 - - + -
61H ILE* 6.3 0.2 - - + -
67H GLU* 6.2 2.7 - - + -
78H ILE* 3.5 17.9 + - + +
79H LEU* 4.6 8.7 - - + +
80H GLU 3.3 1.0 - - - -
81H ILE* 1.3 80.9 - - + +
83H LEU* 1.3 62.2 + - + +
84H ASN 3.3 0.2 - - - -
85H LEU* 3.6 23.5 - - + +
86H LYS* 2.9 34.7 + - + +
171H LEU* 4.3 28.7 - - + -
172H LEU 5.1 5.2 - - - +
173H VAL* 3.7 38.2 - - + +
526J VAL* 5.9 3.4 - - + -
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Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H LEU 3.6 21.1 - - - +
80H GLU* 3.8 12.1 - - - +
81H ILE 3.2 0.6 - - - -
82H LEU* 1.3 76.8 - - + +
84H ASN* 1.3 62.8 + - - +
86H LYS* 3.4 17.3 + - + +
87H GLY* 3.4 7.6 + - - -
128H HIS* 5.5 0.2 + - - -
526J VAL* 3.7 27.4 - - + -
527J LEU 3.7 22.2 - - - +
528J THR* 3.4 30.7 + - - +
550J VAL 5.1 0.2 - - - -
551J ARG* 3.7 39.9 - - + +
569J LEU* 4.1 15.7 - - + -
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Residues in contact with ASN 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H GLU* 6.1 0.9 - - - +
80H GLU* 3.7 7.1 - - - +
81H ILE* 3.3 8.4 + - - +
82H LEU 3.3 0.2 - - - -
83H LEU* 1.3 77.5 - - - +
85H LEU* 1.3 58.2 + - - +
87H GLY 3.3 1.0 + - - -
88H LEU* 3.1 24.1 + - - +
128H HIS* 3.1 25.4 + - + -
129H VAL* 3.0 29.1 + - - +
130H ILE* 3.2 24.9 - - + +
551J ARG* 3.0 35.5 + - - +
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Residues in contact with LEU 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H VAL* 3.6 26.4 - - + +
59H VAL* 3.9 23.1 - - + -
81H ILE* 3.5 18.6 - - + +
82H LEU* 3.3 33.5 + - + +
84H ASN* 1.3 75.1 - - - +
86H LYS* 1.3 64.5 + - - +
88H LEU* 3.8 21.1 + - + +
102H LEU* 5.4 3.4 - - + -
130H ILE* 3.8 27.8 - - + -
142H MET* 4.4 10.8 - - - -
144H ILE* 3.7 22.9 - - + -
173H VAL* 5.0 4.0 - - + +
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Residues in contact with LYS 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H ALA* 5.4 4.2 - - - +
56H VAL* 5.7 1.5 + - - +
82H LEU* 2.9 20.3 + - + +
83H LEU* 3.6 17.0 - - + +
84H ASN 3.2 0.2 - - - -
85H LEU* 1.3 79.4 - - - +
87H GLY* 1.3 60.1 + - - +
88H LEU 3.2 6.9 + - - +
152H TYR* 3.8 3.7 + - - -
173H VAL* 3.8 17.9 - - + -
174H ASP* 3.4 48.0 + - + +
176H CYS* 3.7 24.8 - - - -
526J VAL* 3.5 17.3 + - + +
527J LEU* 4.0 0.4 - - - +
528J THR* 3.9 9.6 - - + +
532J GLU* 2.4 43.3 + - - -
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Residues in contact with GLY 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H LEU 3.4 6.6 + - - -
84H ASN 3.3 8.1 + - - -
86H LYS* 1.3 75.9 - - - +
88H LEU* 1.3 59.4 + - - +
89H ALA* 3.0 14.2 + - - +
125H LYS* 5.4 5.7 + - - +
128H HIS* 4.3 18.0 + - - -
176H CYS* 5.6 1.3 - - - -
181H GLU* 5.9 3.4 - - - -
208H ASN* 5.8 1.2 - - - +
528J THR* 5.1 7.5 + - - +
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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