Contacts of the helix formed by residues 70 - 85 (chain B) in PDB entry 1CF7
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 GLY 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 1.3 80.6 - - - +
71B LEU* 1.3 67.9 + - - -
72B ARG* 3.1 3.8 - - - -
73B HIS 2.8 14.2 + - - -
74B PHE* 3.1 20.9 + - - -
122B ARG* 5.6 1.3 - - - -
607D G 3.2 35.4 - - - -
608D C 5.5 0.4 + - - -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ARG* 6.3 0.2 - - - +
60A ASP* 3.3 43.5 - - + +
63A ASN* 3.7 24.7 - - + +
64A VAL* 4.0 5.6 - - + -
70B GLY* 1.3 70.0 - - - -
72B ARG* 1.3 62.6 + - - +
74B PHE* 3.1 6.9 + - + +
75B SER* 2.8 43.1 + - - +
122B ARG* 4.5 24.5 - - + +
125B ASP* 4.3 15.0 - - + +
126B ALA* 4.3 23.3 - - + +
607D G 3.1 10.6 + - - +
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ASN* 3.0 41.5 + - + +
66A GLU* 2.5 51.6 + - - -
67A GLY* 3.6 23.5 - - - +
73A LYS* 4.0 14.4 - - - +
69B LYS 5.4 1.3 - - - +
70B GLY 3.1 1.5 + - - -
71B LEU* 1.3 81.1 - - - +
73B HIS* 1.3 62.3 + - - +
75B SER* 3.8 1.0 + - - -
76B MET* 3.8 9.4 + - - +
606D C 2.6 33.7 + - - -
607D G 4.7 7.4 + - - +
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Residues in contact with HIS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY* 3.4 39.8 + - - +
69B LYS* 3.3 20.7 + - - +
70B GLY 2.8 9.8 + - - +
72B ARG* 1.3 76.5 - - - +
74B PHE* 1.3 81.0 + + - +
76B MET* 3.7 17.8 + - + +
77B LYS* 3.5 39.7 + - + +
101B PHE* 5.6 3.4 - + - -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 4.3 11.2 - - + -
70B GLY 3.1 31.3 + - - -
71B LEU* 3.1 8.9 + - + +
73B HIS* 1.3 97.1 - + - +
75B SER* 1.3 60.3 + - - +
76B MET 3.1 2.5 - - - -
77B LYS* 3.1 7.6 + - + +
78B VAL* 2.9 36.3 + - + +
97B LEU* 4.6 16.4 - - + -
101B PHE* 4.2 26.5 - + + -
118B ASN* 5.7 2.9 - - - -
119B ILE* 4.0 37.5 - - + -
122B ARG* 4.3 32.1 - - + -
123B VAL* 5.7 2.2 - - + -
126B ALA* 5.0 1.6 - - + -
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Residues in contact with SER 75 (chain B).
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* 3.1 48.2 - - - +
67A GLY* 5.0 0.9 - - - -
68A ILE* 3.7 5.9 - - - +
71B LEU* 2.8 31.0 + - - +
72B ARG 4.1 4.5 - - - -
74B PHE* 1.3 76.4 - - - +
76B MET* 1.3 57.4 + - - +
78B VAL* 3.7 1.7 - - - +
79B CYS* 3.0 30.8 + - - +
126B ALA* 3.9 15.3 - - - +
130B LEU* 4.6 1.8 - - - +
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLY* 3.8 23.1 - - - +
68A ILE* 4.4 7.2 - - + +
72B ARG 3.8 7.0 + - - +
73B HIS* 3.7 21.4 + - + +
74B PHE 3.1 0.4 - - - -
75B SER* 1.3 79.7 - - - +
77B LYS* 1.3 81.0 + - + +
79B CYS* 4.0 1.3 - - - +
80B GLU* 3.0 60.2 + - + +
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B HIS* 3.5 38.3 + - + +
74B PHE* 3.1 13.2 + - + +
76B MET* 1.3 90.1 - - + +
78B VAL* 1.3 63.1 + - - +
80B GLU* 3.7 20.1 + - - +
81B LYS* 3.0 26.2 + - - +
97B LEU* 3.6 27.5 - - + +
100B GLU* 4.1 21.2 + - - +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 2.9 21.3 + - + +
75B SER* 3.7 6.5 - - - +
77B LYS* 1.3 75.6 - - - +
79B CYS* 1.3 64.7 + - - +
81B LYS* 3.2 7.5 + - - +
82B VAL* 3.1 30.1 + - + +
93B VAL* 4.5 7.6 - - + -
97B LEU* 3.9 16.4 - - + -
123B VAL* 4.2 19.7 - - + -
126B ALA* 4.1 17.3 - - + -
127B LEU* 4.2 22.2 - - + -
130B LEU* 3.7 20.6 - - + -
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Residues in contact with CYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.4 28.7 - - + -
75B SER 3.0 16.5 + - - +
76B MET 4.1 2.5 - - - +
78B VAL* 1.3 82.9 - - - +
80B GLU* 1.3 60.6 + - + +
82B VAL* 4.9 2.7 - - - -
83B GLN* 3.4 21.7 + - - +
130B LEU* 4.1 16.2 - - + -
135B ILE* 4.6 1.3 - - - -
145B TRP* 3.8 29.4 - - - -
148B LEU* 4.6 11.2 - - - -
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B MET* 3.0 55.1 + - + +
77B LYS* 3.7 24.7 + - - +
78B VAL 3.2 0.2 - - - -
79B CYS* 1.3 72.8 - - + +
81B LYS* 1.3 68.3 + - - +
83B GLN* 3.3 5.9 + - - +
84B ARG* 2.9 26.9 + - - +
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS 3.0 13.7 + - - +
78B VAL* 3.4 7.4 - - - +
80B GLU* 1.3 80.8 - - + +
82B VAL* 1.3 58.0 + - + +
84B ARG* 3.3 4.9 + - + +
85B LYS* 2.8 46.2 + - + +
88B THR* 5.6 0.9 - - + -
92B GLU 5.4 0.2 - - - -
93B VAL* 4.6 25.8 - - + -
96B GLU* 2.8 47.4 + - - +
97B LEU* 4.4 12.3 - - + -
100B GLU* 2.8 28.1 + - - +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B VAL* 3.1 24.7 + - + +
79B CYS* 4.3 3.8 - - - +
81B LYS* 1.3 73.0 - - - +
83B GLN* 1.3 68.0 + - - +
85B LYS* 3.0 2.1 + - - +
86B GLY* 2.8 23.5 + - - +
88B THR* 4.2 18.2 - - + -
93B VAL* 4.5 9.2 - - + -
127B LEU* 5.0 4.0 - - + -
130B LEU* 6.0 0.2 - - + -
136B ILE* 3.7 28.9 - - + -
143B ILE* 4.0 24.7 - - + -
144B LYS* 4.2 0.9 - - - -
145B TRP* 3.8 22.6 - - + +
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Residues in contact with GLN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B CYS 3.4 14.4 + - - +
80B GLU* 3.3 6.5 + - - +
82B VAL* 1.3 79.9 - - - +
84B ARG* 1.3 66.1 + - - +
85B LYS 3.1 0.2 + - - -
86B GLY* 3.1 10.6 + - - -
145B TRP* 2.9 62.7 - - + +
148B LEU* 5.9 1.0 - - - +
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLU 2.9 18.5 + - - +
81B LYS* 3.7 6.1 - - + +
83B GLN* 1.3 78.4 - - - +
85B LYS* 1.3 62.9 + - + +
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 2.8 32.7 + - + +
82B VAL 3.0 2.2 + - - +
84B ARG* 1.3 83.3 - - + +
86B GLY* 1.3 52.1 + - - +
87B THR* 2.6 29.4 + - - +
88B THR* 4.0 12.6 - - + +
92B GLU* 3.6 35.8 + - + +
93B VAL* 6.1 0.2 - - + -
96B GLU* 2.9 30.4 + - - -
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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