Contacts of the helix formed by residues 74 - 84 (chain L) in PDB entry 4G7Z
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 74 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64L GLU* 5.6 0.7 - - - +
67L THR* 4.4 22.2 - - - +
68L ILE 5.2 1.1 - - - +
72L LYS 3.5 3.6 + - - +
73L GLU* 1.3 78.1 - - - +
75L VAL* 1.3 66.2 + - - +
76L VAL* 3.4 10.6 + - + +
77L GLU* 2.7 39.1 + - - +
78L ILE* 3.1 12.4 + - - +
872N ARG* 2.8 29.2 + - - -
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Residues in contact with VAL 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L ILE* 5.1 8.7 - - + -
61L VAL* 4.1 19.1 - - + -
64L GLU* 3.3 30.9 + - + +
66L SER 3.0 29.4 - - - +
67L THR* 4.4 1.3 - - - -
68L ILE* 4.3 17.1 - - + +
74L ASP* 1.3 71.8 - - - +
76L VAL* 1.3 63.7 + - - +
78L ILE* 3.2 14.2 + - + +
79L ILE* 3.0 32.4 + - + +
165L ILE* 4.1 16.6 - - + -
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Residues in contact with VAL 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L GLU* 3.3 29.2 - - + +
74L ASP* 3.2 10.7 - - + +
75L VAL* 1.3 73.1 - - - +
77L GLU* 1.3 66.8 + - - +
78L ILE 3.0 0.2 + - - -
79L ILE* 3.0 19.0 + - + +
80L LEU* 2.9 39.1 + - + +
842N VAL* 4.0 22.9 - - + -
872N ARG* 4.0 17.5 - - - +
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Residues in contact with GLU 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L GLU* 3.8 21.1 - - + -
74L ASP* 2.7 23.7 + - - +
76L VAL* 1.3 72.6 - - - +
78L ILE* 1.3 56.4 + - - +
80L LEU* 3.6 7.3 - - - +
81L ASN* 2.7 39.4 + - - +
867N ARG* 3.1 38.0 + - - -
870N GLY* 4.9 8.2 - - - +
872N ARG* 3.1 28.7 + - - +
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Residues in contact with ILE 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L ILE* 5.9 3.1 - - + -
68L ILE* 3.8 25.1 - - + -
71L VAL* 4.6 1.8 - - + -
73L GLU* 3.4 38.6 - - + +
74L ASP 3.1 13.0 - - - +
75L VAL* 3.4 7.2 - - - +
76L VAL 3.0 0.8 - - - -
77L GLU* 1.3 73.7 - - - +
79L ILE* 1.3 62.8 + - + +
80L LEU 3.1 1.8 - - - -
81L ASN* 3.1 9.2 + - - +
82L LEU* 3.0 32.4 + - + +
129L ILE* 3.8 29.8 - - + +
130L ALA* 4.5 8.1 - - + -
138L LEU* 5.6 4.0 - - + -
140L MET* 4.4 15.5 - - + -
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Residues in contact with ILE 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L VAL* 5.5 5.8 - - + -
58L ILE* 6.4 1.3 - - + -
64L GLU* 5.4 6.3 - - + -
75L VAL* 3.0 26.1 + - + +
76L VAL* 3.0 31.8 + - + +
78L ILE* 1.3 77.6 - - + +
80L LEU* 1.3 66.3 + - + +
82L LEU* 3.3 18.0 + - + +
83L LYS* 3.1 36.9 + - - +
165L ILE* 5.0 10.5 - - + -
166L PRO 5.9 1.1 - - - +
167L VAL* 3.8 28.3 - - + +
168L ASP* 5.6 2.2 - - - +
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Residues in contact with LEU 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L VAL* 2.9 33.5 + - + +
77L GLU* 3.6 11.9 - - - +
79L ILE* 1.3 84.8 - - + +
81L ASN* 1.3 66.1 + - - +
82L LEU 3.0 1.1 - - - -
83L LYS* 2.9 25.0 + - - +
84L GLU* 3.3 7.8 + - - +
842N VAL* 3.8 35.7 - - + +
843N PHE 4.2 0.4 - - - +
844N ALA* 3.4 25.1 - - - +
867N ARG* 3.4 42.2 - - + +
872N ARG* 5.1 5.6 - - + +
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Residues in contact with ASN 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L GLU* 5.6 0.3 - - - +
77L GLU* 2.7 29.3 + - - +
78L ILE 3.1 9.1 + - - +
80L LEU* 1.3 78.3 - - - +
82L LEU* 1.3 56.6 + - - +
84L GLU* 3.1 25.0 + - - +
85L LEU* 3.4 5.5 + - - +
127L LEU* 3.5 19.6 - - + +
128L HIS* 3.3 35.3 + - - +
129L ILE* 3.8 20.1 - - + +
867N ARG* 3.1 24.7 + - - +
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Residues in contact with LEU 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L VAL* 3.5 22.8 - - + +
56L VAL* 3.6 33.9 - - + -
78L ILE* 3.0 27.0 + - + +
79L ILE* 3.3 21.1 - - + +
80L LEU 3.0 0.2 - - - -
81L ASN* 1.3 73.8 - - - +
83L LYS* 1.3 65.1 + - - +
84L GLU 3.0 1.8 - - - -
85L LEU* 3.0 34.1 + - + +
114L PHE* 4.4 15.0 - - + -
129L ILE* 5.4 9.4 - - + -
140L MET* 4.7 6.3 - - - -
142L VAL* 3.8 23.3 - - + -
167L VAL* 5.5 1.3 - - + -
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Residues in contact with LYS 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L VAL* 5.3 3.8 - - - +
79L ILE* 3.1 23.5 + - - +
80L LEU* 2.9 18.1 + - - +
82L LEU* 1.3 76.5 - - - +
84L GLU* 1.3 59.7 + - - +
85L LEU 3.2 5.8 + - - +
167L VAL* 3.7 20.6 - - + -
168L ASP* 2.8 43.2 + - - +
170L VAL* 4.3 27.1 - - + +
175L ARG* 4.9 4.7 + - - -
842N VAL* 2.7 30.1 + - - +
843N PHE* 5.5 0.4 - - - -
844N ALA* 4.1 11.7 - - + -
845N ASN* 5.6 1.5 + - - +
848N GLU* 3.1 29.9 + - - +
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Residues in contact with GLU 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L LEU 3.3 8.5 + - - +
81L ASN* 3.1 12.2 + - - +
82L LEU 3.0 0.8 - - - -
83L LYS* 1.3 77.7 - - - +
85L LEU* 1.3 61.6 + - - +
86L VAL* 3.4 9.4 + - - +
124L ASN* 3.3 14.4 + - - -
127L LEU* 3.8 19.4 - - + +
175L ARG* 4.4 9.3 + - - +
844N ALA* 3.7 11.3 - - + +
845N ASN* 3.5 28.5 + - - +
867N ARG* 3.0 38.0 + - - -
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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