Contacts of the helix formed by residues 90 - 102 (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 TYR 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B SER* 1.4 73.3 - - - +
91B ASN* 1.3 83.4 + - - +
93B VAL* 3.3 4.9 + - - +
94B ALA* 2.8 41.7 + - + +
120B ARG* 2.9 41.5 + - + +
123B VAL* 4.0 15.4 - - + +
124B TYR* 3.0 58.2 + + - -
127B LEU* 3.9 15.9 - - + -
138B LYS* 4.8 7.0 - - - +
141B LYS 5.0 1.0 + - - -
143B ILE* 3.6 17.9 - - + +
504C T 3.7 16.6 - - - +
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Residues in contact with ASN 91 (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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89B SER* 3.1 6.9 + - - +
90B TYR* 1.3 101.8 - - - +
92B GLU* 1.3 65.3 + - - +
94B ALA* 4.7 1.7 - - - +
95B ASP* 3.0 47.3 + - - +
120B ARG* 4.8 7.8 + - - -
503C T 5.6 4.9 + - - -
504C T 4.6 5.1 + - - -
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Residues in contact with GLU 92 (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* 5.4 0.2 - - - -
85B LYS* 3.6 29.1 + - + +
87B THR 4.5 2.1 - - - +
88B THR* 2.7 33.2 + - - +
89B SER* 3.0 15.9 + - - +
91B ASN* 1.3 76.3 - - - +
93B VAL* 1.3 66.2 + - - +
95B ASP* 4.2 2.8 - - - +
96B GLU* 3.2 37.6 + - + +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 4.5 28.0 - - + -
81B LYS* 4.6 25.4 - - + -
82B VAL* 4.5 10.3 - - + -
85B LYS* 6.1 0.2 - - + -
88B THR* 3.7 24.9 - - + +
89B SER 2.9 17.0 + - - +
90B TYR* 3.6 6.3 - - - +
92B GLU* 1.3 79.3 - - + +
94B ALA* 1.3 66.3 + - - +
96B GLU* 3.3 2.8 + - - +
97B LEU* 3.1 29.9 + - + +
123B VAL* 4.5 10.1 - - + -
127B LEU* 5.6 2.9 - - + -
143B ILE* 5.1 4.3 - - + -
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Residues in contact with ALA 94 (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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90B TYR* 2.8 44.8 + - + +
91B ASN* 4.2 2.0 - - - +
93B VAL* 1.3 73.5 - - - +
95B ASP* 1.3 68.2 + - - +
97B LEU* 3.0 4.1 + - - +
98B VAL* 2.9 29.1 + - + +
120B ARG* 4.5 14.8 - - + +
123B VAL* 4.4 21.3 - - + -
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASN* 3.0 36.4 + - - +
92B GLU* 4.2 3.2 - - - +
94B ALA* 1.3 77.6 - - - +
96B GLU* 1.3 58.5 + - + +
98B VAL* 3.4 6.7 + - - +
99B SER* 2.9 30.4 + - - -
116B GLN* 5.3 0.3 + - - -
120B ARG* 3.0 30.4 + - - -
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Residues in contact with GLU 96 (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 37.9 + - - +
85B LYS* 2.9 33.6 + - - -
92B GLU* 3.2 23.9 + - + +
93B VAL 3.8 1.1 - - - +
94B ALA 3.2 0.4 - - - -
95B ASP* 1.3 77.0 - - + +
97B LEU* 1.3 66.3 + - - +
99B SER* 3.9 6.4 - - - -
100B GLU* 3.2 29.3 + - - +
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Residues in contact with LEU 97 (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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74B PHE* 4.3 14.7 - - + +
77B LYS* 3.6 38.4 - - + +
78B VAL* 3.9 24.9 - - + +
81B LYS* 4.4 19.3 - - + -
93B VAL* 3.1 16.7 + - + +
94B ALA* 3.0 7.2 + - - +
96B GLU* 1.3 76.6 - - - +
98B VAL* 1.3 66.1 + - - +
100B GLU* 3.4 14.7 + - - +
101B PHE* 3.0 25.5 + - - +
119B ILE* 4.1 14.3 - - + +
123B VAL* 4.2 13.0 - - + -
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Residues in contact with VAL 98 (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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94B ALA* 2.9 22.1 + - - +
95B ASP* 3.6 7.6 - - - +
97B LEU* 1.3 76.2 - - - +
99B SER* 1.3 57.9 + - - +
101B PHE* 3.3 1.2 + - - +
102B THR* 2.8 43.2 + - - +
116B GLN* 3.9 47.3 - - + +
119B ILE* 3.8 34.0 - - + +
120B ARG* 4.9 7.9 - - + +
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Residues in contact with SER 99 (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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95B ASP 2.9 18.2 + - - -
96B GLU* 3.9 7.0 - - - -
98B VAL* 1.3 79.6 - - - +
100B GLU* 1.3 57.0 + - - +
102B THR* 3.4 5.0 + - - -
103B ASN* 2.9 42.8 + - - +
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Residues in contact with GLU 100 (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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77B LYS* 4.1 24.5 + - - +
81B LYS* 2.8 30.5 + - - +
96B GLU* 3.2 19.8 + - - +
97B LEU* 3.8 11.9 - - - +
98B VAL 3.3 0.2 - - - -
99B SER* 1.3 72.8 - - - +
101B PHE* 1.3 67.4 + - - +
103B ASN* 3.2 14.1 + - - +
104B SER* 3.4 9.0 + - - -
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Residues in contact with PHE 101 (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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68B GLY 4.0 7.6 - - - -
69B LYS* 3.4 43.1 - - + -
73B HIS* 5.6 2.7 - + - -
74B PHE* 4.2 19.5 - + + -
97B LEU 3.0 18.3 + - - +
98B VAL 3.7 3.1 - - - +
100B GLU* 1.3 75.9 - - - +
102B THR* 1.3 66.5 + - - +
104B SER* 3.1 25.9 + - - -
107B HIS* 3.9 16.0 - + - +
115B ASP* 3.0 35.2 - - + -
119B ILE* 3.7 18.4 - - + -
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Residues in contact with THR 102 (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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98B VAL* 2.8 28.2 + - - +
99B SER* 3.7 5.4 - - - -
101B PHE* 1.3 81.2 - - - +
103B ASN* 1.3 69.7 + - - +
104B SER 3.2 2.4 + - - +
107B HIS* 3.5 29.2 + - + +
112B SER* 4.1 29.2 + - - +
115B ASP* 5.6 1.9 - - - +
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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