Contacts of the helix formed by residues 113 - 132 (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 ALA 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA 4.8 0.8 + - - +
111B ASP 3.5 0.4 - - - -
112B SER* 1.3 73.4 - - - +
114B TYR* 1.3 77.4 + - + +
116B GLN* 3.6 11.4 - - - +
117B LYS* 3.2 36.7 + - - +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA 3.5 21.5 - - - -
111B ASP* 2.5 23.8 - - + +
112B SER 2.4 9.7 - - - +
113B ALA* 1.3 83.5 - - + +
115B ASP* 1.3 74.2 + - - +
117B LYS* 4.5 9.2 - - - +
609D G 4.9 17.7 - - - +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 4.4 13.0 + - - -
101B PHE* 3.0 36.1 - - + -
102B THR* 5.6 2.5 - - - +
107B HIS* 3.3 18.2 + - - +
111B ASP* 3.2 20.3 - - - +
112B SER* 3.6 4.7 - - - +
114B TYR* 1.3 80.9 - - - +
116B GLN* 1.3 56.4 + - - +
117B LYS 3.2 0.2 - - - -
118B ASN* 3.5 20.8 - - - +
119B ILE* 2.5 44.8 + - + +
609D G 5.3 0.6 + - - -
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASP* 5.3 0.4 + - - -
98B VAL* 3.9 35.1 - - + +
102B THR* 6.0 0.2 + - - -
112B SER 2.9 19.6 + - - +
113B ALA* 3.6 10.8 - - - +
115B ASP* 1.3 76.5 - - - +
117B LYS* 1.3 70.2 + - + +
119B ILE* 4.0 1.2 - - - +
120B ARG* 3.0 70.8 + - - +
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 3.2 22.9 + - - +
114B TYR* 4.7 6.5 - - - -
116B GLN* 1.3 84.9 + - + +
118B ASN* 1.3 62.4 + - - +
120B ARG* 3.3 10.8 + - - +
121B ARG* 3.1 22.0 + - - +
609D G 6.1 5.2 - - + +
610D C 5.8 3.6 - - - +
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Residues in contact with ASN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 5.6 1.5 + - - +
74B PHE* 5.7 2.6 - - - -
115B ASP* 3.1 20.8 + - - +
117B LYS* 1.3 78.9 - - - +
119B ILE* 1.3 66.8 + - + +
121B ARG* 3.3 5.6 + - - +
122B ARG* 3.0 42.9 + - - +
607D G 5.5 0.2 - - - +
608D C 3.3 44.9 + - - +
609D G 3.1 35.4 + - - +
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 4.0 29.6 - - + -
94B ALA* 4.9 1.1 - - - +
97B LEU* 4.1 20.2 - - + +
98B VAL* 3.8 33.4 - - + +
101B PHE* 3.7 41.7 - - + -
115B ASP* 2.5 28.7 + - + +
118B ASN* 1.3 71.9 - - + +
120B ARG* 1.3 58.5 + - - +
122B ARG* 3.0 10.2 + - - +
123B VAL* 2.9 37.2 + - + +
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 2.9 36.1 + - + +
91B ASN* 4.8 8.8 + - - -
94B ALA* 4.5 14.9 - - + +
95B ASP* 3.0 26.5 + - - -
98B VAL* 4.9 5.5 - - + +
116B GLN* 3.0 57.2 + - + +
117B LYS* 3.4 13.7 - - - +
119B ILE* 1.3 76.8 - - - +
121B ARG* 1.3 62.3 + - - +
123B VAL* 3.6 6.2 + - - -
124B TYR* 3.4 10.4 + - + -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS 3.1 13.7 + - - +
118B ASN* 3.3 7.2 + - - +
120B ARG* 1.3 75.6 - - - +
122B ARG* 1.3 83.4 + - - +
124B TYR* 3.4 15.7 + - - +
125B ASP* 3.0 45.0 + - - +
505C C 3.7 44.6 + - - +
506C G 3.0 44.2 + - - -
507C C 3.8 9.7 - - - +
609D G 4.0 15.6 + - + +
610D C 4.3 3.6 - - - +
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ARG* 5.9 0.8 - - - +
60A ASP* 5.4 1.6 + - - -
70B GLY* 5.6 0.7 - - - -
71B LEU* 4.5 25.9 - - + +
74B PHE* 4.3 32.5 - - + -
118B ASN* 3.0 35.9 + - - +
119B ILE* 3.0 8.4 + - - +
121B ARG* 1.3 91.9 - - - +
123B VAL* 1.3 65.3 + - - +
125B ASP* 2.8 47.1 + - - +
126B ALA* 3.3 10.9 + - - +
607D G 5.7 1.8 - - - -
608D C 3.0 29.0 - - - +
609D G 2.9 42.4 + - - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 5.7 3.1 - - + -
78B VAL* 4.2 12.1 - - + -
90B TYR* 4.0 13.5 - - + -
93B VAL* 4.5 10.3 - - + -
94B ALA* 4.4 15.0 - - + -
97B LEU* 4.2 25.1 - - + -
119B ILE* 2.9 27.4 + - + +
120B ARG 4.0 5.8 - - - +
121B ARG 3.3 0.6 - - - -
122B ARG* 1.3 76.4 - - + +
124B TYR* 1.3 62.5 + - - +
126B ALA* 3.3 6.8 + - - +
127B LEU* 2.9 46.1 + - + +
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.0 49.0 - + - -
120B ARG* 3.4 18.2 - - + -
121B ARG* 3.4 14.9 + - - +
122B ARG 3.2 0.8 - - - -
123B VAL* 1.3 76.0 - - - +
125B ASP* 1.3 65.8 + - - +
127B LEU* 3.4 5.7 + - + +
128B ASN* 3.0 32.2 + - - +
138B LYS* 5.5 5.2 - - - -
503C T 3.9 6.2 - - - +
504C T 2.5 74.1 + + + +
505C C 3.7 42.8 - + + +
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 24.5 - - + +
60A ASP* 4.2 12.6 - - - +
64A VAL* 5.5 0.7 - - - -
71B LEU* 4.3 17.7 - - + +
121B ARG* 3.0 34.8 + - - +
122B ARG* 2.8 35.8 + - - +
124B TYR* 1.3 79.9 - - - +
126B ALA* 1.3 64.3 + - - +
128B ASN* 3.5 4.6 + - - +
129B VAL* 3.3 25.3 + - - +
505C C 4.9 3.1 - - - +
506C G 5.0 2.4 + - - -
507C C 5.2 1.7 + - - -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 4.6 5.9 - - - +
71B LEU* 4.3 6.6 - - + +
74B PHE* 5.0 1.3 - - + -
75B SER* 3.9 35.2 - - - +
78B VAL* 4.1 17.7 - - + -
122B ARG 3.3 7.6 + - - +
123B VAL* 3.7 6.7 - - - +
124B TYR 3.3 0.2 - - - -
125B ASP* 1.3 76.5 - - - +
127B LEU* 1.3 66.9 - - - +
129B VAL* 3.0 4.9 + - - +
130B LEU* 2.9 28.2 + - + +
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Residues in contact with LEU 127 (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* 4.2 17.7 - - + +
82B VAL* 5.0 3.1 - - + -
90B TYR* 3.9 21.1 - - + -
93B VAL* 5.6 4.3 - - + -
123B VAL* 2.9 41.2 + - + +
124B TYR* 3.9 6.7 - - + +
126B ALA* 1.3 75.0 - - - +
128B ASN* 1.3 58.3 + - - +
130B LEU* 3.3 6.1 + - - +
131B MET* 2.7 46.5 + - + +
136B ILE* 3.9 21.5 - - + +
138B LYS* 5.7 4.9 - - + +
143B ILE* 3.9 31.4 - - + -
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Residues in contact with ASN 128 (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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21A SER* 6.0 2.2 - - - -
22A LEU* 5.0 6.9 - - + +
23A GLY* 4.1 18.0 - - - +
124B TYR* 3.0 20.0 + - - +
125B ASP* 3.8 7.9 + - - +
127B LEU* 1.3 81.4 - - - +
129B VAL* 1.3 61.4 + - - +
131B MET* 3.5 21.7 - - - +
132B ALA* 3.3 20.4 + - - +
138B LYS* 5.8 0.7 - - - -
505C C 3.2 49.7 + - - +
506C G 4.8 6.5 + - - -
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.0 22.7 - - + -
26A THR* 3.9 28.7 - - + +
60A ASP 4.6 1.8 - - - +
61A ILE* 4.7 7.0 - - + +
64A VAL* 3.0 48.7 - - + -
65A LEU* 5.1 5.6 - - + +
125B ASP 3.3 13.6 + - - +
126B ALA 3.0 3.4 + - - +
128B ASN* 1.3 73.6 - - - +
130B LEU* 1.3 73.6 + - + +
131B MET 3.0 1.6 - - - -
132B ALA* 3.1 3.0 + - - +
133B MET* 2.9 33.4 + - + +
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Residues in contact with LEU 130 (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* 4.1 13.7 - - + -
65A LEU* 6.2 1.6 - - + -
68A ILE* 4.0 28.7 - - + -
75B SER 4.6 2.2 - - - +
78B VAL* 3.7 30.3 - - + -
79B CYS* 4.1 19.7 - - + -
126B ALA* 2.9 18.3 + - + +
127B LEU* 3.5 4.0 - - - +
129B VAL* 1.3 80.3 - - + +
131B MET* 1.3 61.2 + - - +
133B MET* 3.3 9.8 + - + +
135B ILE* 3.2 48.0 + - + +
136B ILE* 3.7 21.5 + - + -
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Residues in contact with MET 131 (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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127B LEU* 2.7 29.0 + - + +
128B ASN* 3.5 28.9 - - - +
130B LEU* 1.3 76.6 - - - +
132B ALA* 1.3 54.3 + - - +
134B ASN* 2.7 28.2 + - - -
136B ILE* 3.9 16.3 - - + +
137B SER 4.2 13.9 - - - +
138B LYS* 2.9 48.9 - - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY* 3.5 27.4 - - - +
26A THR* 3.7 15.7 - - + +
27A THR* 4.4 12.8 + - - +
30A VAL* 5.8 1.6 - - - +
128B ASN 3.3 10.2 + - - +
129B VAL 3.1 8.4 + - - +
131B MET* 1.3 79.9 - - - +
133B MET* 1.3 59.7 + - - +
134B ASN* 3.1 2.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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