Contacts of the helix formed by residues 69 - 87 (chain B) in PDB entry 3IFA
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 GLN 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 6.0 4.0 - - - +
70B VAL* 1.3 71.3 + - - +
71B LYS* 3.9 22.9 - - - +
72B LYS* 3.8 42.8 + - + +
73B LEU* 3.2 21.7 + - - +
126B ILE* 5.6 0.9 - - - -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLN* 1.3 77.6 - - - +
71B LYS* 1.3 58.9 + - - +
73B LEU* 3.3 7.7 + - - +
74B ASP* 2.9 42.3 + - - +
123B SER* 3.1 30.4 - - - +
124B SER* 4.3 11.0 - - - +
126B ILE* 3.5 25.5 - - + +
127B ASP* 4.9 7.6 - - + +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLN* 3.3 21.5 - - - +
70B VAL* 1.3 78.8 - - - +
72B LYS* 1.3 70.2 - - + +
74B ASP* 3.4 9.0 + - - +
75B VAL* 3.0 53.4 + - + +
98B GLU* 5.2 5.7 + - - -
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Residues in contact with LYS 72 (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 GLN* 3.5 42.0 + - + +
70B VAL 3.4 0.4 - - - -
71B LYS* 1.3 84.0 - - + +
73B LEU* 1.3 58.1 + - - +
75B VAL* 3.3 6.1 + - + +
76B LEU* 2.9 30.3 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 3.7 35.7 - - + +
48B VAL* 4.2 18.6 - - + +
50B LYS* 4.6 11.7 - - + +
69B GLN 3.2 11.2 + - - +
70B VAL* 3.3 8.0 + - - +
72B LYS* 1.3 76.5 - - - +
74B ASP* 1.3 59.6 + - - +
76B LEU* 4.3 10.5 - - + -
77B SER* 2.8 40.9 + - - +
120B LEU* 3.6 14.1 - - + -
126B ILE* 3.5 34.8 - - + -
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 2.9 26.6 + - - +
71B LYS* 3.5 13.4 - - - +
73B LEU* 1.3 75.0 - - - +
75B VAL* 1.3 58.9 + - + +
77B SER* 3.8 2.4 - - - -
78B ASN* 3.0 30.5 + - - +
98B GLU* 3.6 32.4 - - - +
119B PRO* 4.8 1.6 - - - +
120B LEU* 4.0 11.7 - - - +
123B SER* 2.6 37.0 + - - -
341B SO4 5.3 1.2 + - - -
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 3.0 48.9 + - + +
72B LYS* 3.7 6.1 - - - +
74B ASP* 1.3 73.5 - - - +
76B LEU* 1.3 59.3 + - - +
78B ASN* 3.4 6.7 + - - +
79B SER* 2.9 40.8 + - - +
98B GLU* 4.5 9.2 - - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 4.0 26.9 - - + -
72B LYS 2.9 17.4 + - - +
73B LEU* 3.9 10.3 - - + +
74B ASP 3.4 0.2 - - - -
75B VAL* 1.3 78.4 - - - +
77B SER* 1.3 58.9 + - - +
79B SER* 3.2 7.6 + - - -
80B LEU* 2.9 49.5 + - + +
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Residues in contact with SER 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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44B ILE* 3.7 28.1 - - - +
47B ALA* 5.9 0.2 - - - +
73B LEU* 2.8 27.1 + - - +
74B ASP 3.8 3.6 - - - -
76B LEU* 1.3 75.5 - - - +
78B ASN* 1.3 62.6 + - - +
80B LEU* 3.3 4.0 + - - +
81B VAL* 3.1 28.9 + - - +
119B PRO* 3.9 22.4 - - - -
120B LEU* 3.6 20.1 - - - +
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Residues in contact with ASN 78 (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 ASP 3.0 18.4 + - - +
75B VAL* 3.5 6.9 - - - +
76B LEU 3.3 0.2 - - - -
77B SER* 1.3 74.5 - - - +
79B SER* 1.3 59.4 + - - +
81B VAL* 3.4 2.3 + - - +
82B ILE* 2.9 46.3 + - - +
96B SER* 2.6 27.0 + - - -
98B GLU* 3.6 17.6 + - + +
99B ASN* 2.9 27.7 + - - +
117B PHE* 3.6 8.2 - - - -
119B PRO* 3.7 11.9 - - + +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 2.9 27.8 + - - +
76B LEU* 3.7 10.1 - - - -
78B ASN* 1.3 73.6 + - - +
80B LEU* 1.3 65.7 + - - +
82B ILE* 4.2 7.4 - - - +
83B ASN* 3.0 32.9 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA* 4.1 9.2 - - + -
43B ALA* 3.6 33.4 - - + +
44B ILE* 3.7 30.3 - - + +
47B ALA* 5.7 0.4 - - + -
76B LEU* 2.9 42.2 + - + +
77B SER* 3.5 7.0 - - - +
79B SER* 1.3 76.9 - - - +
81B VAL* 1.3 61.9 - - - +
83B ASN* 3.9 2.4 - - - +
84B MET* 3.0 35.4 + - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B MET* 4.0 20.9 - - + -
40B ALA* 3.8 13.9 - - + -
44B ILE* 3.6 22.9 - - + -
77B SER 3.1 16.0 + - - +
78B ASN 4.0 0.2 - - - +
80B LEU* 1.3 74.7 - - - +
82B ILE* 1.3 63.0 + - - +
84B MET* 3.4 0.7 + - - +
85B LEU* 2.9 48.2 + - + +
117B PHE* 3.5 36.1 - - + -
119B PRO* 4.3 11.4 - - + -
134B THR* 4.8 0.2 - - + -
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Residues in contact with ILE 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 ASN* 2.9 47.0 + - - +
79B SER* 4.2 5.6 - - - +
81B VAL* 1.3 74.7 - - - +
83B ASN* 1.3 62.0 + - - +
85B LEU* 4.0 0.2 - - - +
86B GLN* 2.8 65.0 + - - +
94B LEU* 3.9 15.3 - - + -
99B ASN* 4.0 12.1 - - - +
103B ILE* 4.3 15.5 - - + -
117B PHE* 3.9 16.8 - - + -
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Residues in contact with ASN 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 SER* 3.0 22.8 + - - +
80B LEU* 3.9 2.9 - - - +
82B ILE* 1.3 83.1 - - - +
84B MET* 1.3 54.8 + - + +
86B GLN* 4.1 6.7 - - - +
87B SER* 2.7 43.9 + - - -
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Residues in contact with MET 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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11A LEU* 5.2 12.3 - - - -
12A THR* 4.8 5.6 - - + -
15A ARG* 2.8 61.0 + - - +
36B SER* 3.2 29.7 - - - +
39B THR* 3.6 33.2 - - + +
40B ALA* 4.2 14.1 - - + +
80B LEU* 3.0 25.4 + - + +
81B VAL 4.0 1.8 - - - +
83B ASN* 1.3 82.2 - - + +
85B LEU* 1.3 63.3 + - + +
87B SER* 3.6 2.2 - - - -
88B SER 3.2 3.8 + - - -
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Residues in contact with LEU 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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33B LEU* 3.4 24.0 - - + +
36B SER* 4.3 1.3 - - - -
37B MET* 4.0 35.7 - - + +
81B VAL* 2.9 39.9 + - + +
82B ILE 4.0 1.6 - - - +
84B MET* 1.3 75.6 - - - +
86B GLN* 1.3 64.4 + - - +
88B SER* 2.6 25.7 + - - -
89B TYR 4.3 0.2 + - - -
91B THR* 3.4 18.9 + - + +
94B LEU* 3.9 19.5 - - + -
115B VAL* 3.9 29.2 - - + -
117B PHE* 4.3 4.0 - - + -
138B ILE* 6.5 0.2 - - + -
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Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE* 2.8 39.9 + - - +
83B ASN* 4.2 5.9 - - - +
85B LEU* 1.3 75.4 - - - +
87B SER* 1.3 58.4 + - - +
88B SER 3.3 1.2 + - - -
89B TYR 3.4 8.3 + - - -
91B THR* 4.0 6.6 + - - -
94B LEU* 4.0 12.5 - - + +
103B ILE* 3.4 31.5 + - - +
104B ILE 4.8 0.8 + - - -
105B THR* 4.3 28.8 + - + +
106B ALA 5.4 1.5 - - - +
109B LYS* 3.7 28.3 - - + +
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Residues in contact with SER 87 (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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9A ASP* 4.1 18.4 - - - -
10A MET* 3.2 23.9 - - - +
15A ARG* 2.8 32.3 + - - -
83B ASN* 2.7 28.4 + - - -
84B MET* 3.2 2.9 + - - -
86B GLN* 1.3 72.4 - - - +
88B SER* 1.3 63.1 + - - +
89B TYR* 3.2 10.8 - - - -
109B LYS* 4.6 8.3 - - - +
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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
------------------------------------------------------------
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