Contacts of the helix formed by residues 77 - 87 (chain A) in PDB entry 6PB4
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLU* 5.3 1.3 - - - +
69A SER 4.9 5.2 - - - +
70A THR* 4.8 15.8 - - - +
75A GLN 5.2 0.7 - - - +
76A GLU* 1.3 77.4 - - - +
78A ILE* 1.3 65.3 + - - +
79A LEU* 3.3 22.8 + - + +
80A GLU* 3.7 8.6 + - + +
81A ILE* 3.0 29.0 + - - +
729C ALA* 5.0 5.5 - - - +
755C LYS* 4.9 9.6 + - - +
756C TYR* 3.1 28.3 + - - -
766C ASN* 4.3 6.2 + - - -
768C MET* 6.1 0.5 - - - +
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Residues in contact with ILE 78 (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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64A VAL* 3.7 17.7 - - + -
66A HIS 3.1 7.6 - - - +
67A GLU* 3.1 36.3 + - + +
69A SER* 3.0 40.7 + - - +
70A THR* 5.0 4.7 - - - +
77A ASP* 1.3 72.8 - - - +
79A LEU* 1.3 65.5 + - - +
81A ILE* 3.0 22.1 + - - +
82A LEU* 3.0 31.4 + - + +
171A LEU* 4.5 15.9 - - + -
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Residues in contact with LEU 79 (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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67A GLU* 3.1 39.3 - - + +
68A TYR* 5.9 0.2 - - + -
77A ASP* 3.3 31.4 - - + +
78A ILE* 1.3 77.4 - - - +
80A GLU* 1.3 66.4 + - + +
82A LEU* 3.1 12.7 + - + +
83A LEU* 2.8 43.5 + - + +
693C LEU* 4.3 28.3 - - + -
756C TYR* 4.1 5.6 - - - +
831C ILE* 5.2 6.5 - - + -
1057C LYS* 5.9 4.9 - - - +
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Residues in contact with GLU 80 (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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76A GLU* 3.1 36.8 - - + +
77A ASP* 3.8 15.6 + - + +
78A ILE 3.3 0.4 - - - -
79A LEU* 1.3 85.5 - - + +
81A ILE* 1.3 53.3 + - - +
83A LEU* 3.2 4.0 + - - +
84A ASN* 2.6 40.2 + - - +
694C ARG* 3.9 34.6 + - - +
768C MET* 5.9 2.3 - - - +
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Residues in contact with ILE 81 (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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74A VAL* 4.7 4.7 - - + -
76A GLU* 3.6 24.9 - - + +
77A ASP 3.0 23.6 - - - +
78A ILE* 3.0 9.3 + - - +
80A GLU* 1.3 74.1 - - - +
82A LEU* 1.3 64.3 + - + +
83A LEU 3.1 1.3 - - - -
84A ASN* 3.0 10.3 + - - +
85A LEU* 3.0 31.4 + - + +
130A ILE* 3.3 35.9 - - + +
131A CYS* 4.1 18.2 - - + -
140A ILE* 6.4 1.6 - - + -
142A MET* 6.3 3.1 - - + -
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Residues in contact with LEU 82 (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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59A VAL* 4.8 11.2 - - + -
67A GLU* 5.7 0.9 - - + -
78A ILE* 3.0 50.8 + - + +
79A LEU* 3.2 13.7 - - + +
81A ILE* 1.3 78.3 - - + +
83A LEU* 1.3 60.2 + - + +
85A LEU* 3.0 22.0 + - + +
86A LYS* 2.9 25.3 + - - +
171A LEU* 4.8 11.7 - - + -
172A LEU 5.8 0.2 - - - +
173A VAL* 3.5 43.3 - - + +
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Residues in contact with LEU 83 (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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79A LEU* 2.8 37.9 + - + +
80A GLU* 3.5 8.7 - - - +
81A ILE 3.1 0.2 - - - -
82A LEU* 1.3 78.3 - - + +
84A ASN* 1.3 60.6 + - - +
85A LEU 3.0 5.6 + - - -
86A LYS* 3.5 24.2 + - + +
87A GLY* 4.0 6.2 + - - -
128A HIS* 5.5 0.3 - - - -
693C LEU* 5.7 6.5 - - + -
694C ARG* 3.6 24.0 - - - +
824C GLN 5.7 3.4 - - - +
825C GLU 5.9 0.7 - - - +
826C ASP* 4.7 21.5 - - - +
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Residues in contact with ASN 84 (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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76A GLU* 4.7 2.9 - - - +
80A GLU* 2.6 33.8 + - - +
81A ILE* 3.0 13.7 + - - +
83A LEU* 1.3 76.3 - - - +
85A LEU* 1.3 51.0 + - - +
128A HIS* 2.3 39.8 + - - -
129A VAL* 3.6 19.3 + - - +
130A ILE* 3.0 30.9 + - + +
694C ARG* 6.0 0.8 - - - +
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Residues in contact with LEU 85 (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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56A VAL* 5.1 12.8 - - + +
59A VAL* 4.5 20.0 - - + -
81A ILE* 3.0 23.8 + - + +
82A LEU* 3.0 26.4 + - + +
84A ASN* 1.3 78.3 - - - +
86A LYS* 1.3 65.1 + - - +
87A GLY 3.0 2.2 - - - -
88A LEU* 2.9 39.2 - - + +
128A HIS* 3.9 1.6 - - - -
130A ILE* 3.5 31.4 - - + -
142A MET* 5.7 7.6 - - - -
144A ILE* 5.9 5.4 - - + -
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Residues in contact with LYS 86 (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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82A LEU 2.9 12.6 + - - +
83A LEU* 3.5 22.3 + - + +
85A LEU* 1.3 77.7 - - - +
87A GLY* 1.3 58.4 + - - +
88A LEU 3.1 8.5 + - - +
152A TYR* 5.5 3.8 - - - -
173A VAL* 6.1 5.4 - - + -
174A ASP* 4.7 15.3 - - + +
176A CYS* 3.8 33.3 - - - +
821C ARG* 4.2 18.2 - - - +
824C GLN* 4.0 29.7 + - - +
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Residues in contact with GLY 87 (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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83A LEU 4.0 6.4 + - - -
85A LEU 3.0 1.8 - - - -
86A LYS* 1.3 79.0 - - - +
88A LEU* 1.3 57.7 + - - -
89A ALA* 5.6 0.2 - - - +
125A LYS* 6.1 0.5 - - - +
128A HIS* 3.0 28.6 + - - -
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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