Contacts of the helix formed by residues 87 - 105 (chain G) in PDB entry 1RFU
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 87 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56G VAL* 4.9 4.7 - - + -
57G LEU 3.6 11.0 - - - +
58G ASN* 3.3 28.7 - - - +
85G THR* 3.1 6.6 - - + +
86G ARG* 1.3 80.6 - - - +
88G LYS* 1.3 58.3 + - - +
89G SER* 2.6 42.0 + - - -
90G PHE* 3.0 21.3 + - + +
91G LEU* 2.9 25.5 + - - +
132G LEU* 3.8 2.5 - - - -
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Residues in contact with LYS 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ARG 3.9 2.4 + - - -
87G ASP* 1.3 69.5 + - - +
89G SER* 1.3 74.0 + - - +
91G LEU* 3.3 1.4 + - - +
92G ALA* 2.9 28.5 + - + +
131G ASP* 3.6 42.2 + - + +
132G LEU* 3.3 20.7 - - + +
135G VAL* 3.6 19.3 - - + +
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Residues in contact with SER 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G ASN* 5.7 0.2 - - - -
59G SER* 2.9 29.2 - - - -
87G ASP* 2.6 22.9 + - - -
88G LYS* 1.3 85.0 + - - +
90G PHE* 1.3 60.7 + - - -
92G ALA* 3.6 5.8 - - - +
93G MET* 3.0 24.8 + - - +
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Residues in contact with PHE 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ILE* 3.5 33.2 - - + -
38G VAL* 4.4 3.8 - - + -
40G SER* 3.6 25.4 - - - -
57G LEU* 3.9 31.6 - - + -
58G ASN 4.2 6.3 - - - -
59G SER* 4.3 7.8 - - - +
62G LEU* 3.4 40.0 - - + +
85G THR* 3.4 27.8 - - + -
87G ASP* 3.0 21.5 + - + +
89G SER* 1.3 81.6 - - - +
91G LEU* 1.3 63.7 + - - +
93G MET* 3.3 3.9 + - - +
94G VAL* 2.9 32.2 + - + +
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Residues in contact with LEU 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G THR* 5.7 4.7 - - - +
83G GLY 5.4 0.9 - - - +
85G THR* 4.6 9.9 - - + +
87G ASP 2.9 12.0 + - - +
88G LYS 3.7 6.7 - - - +
90G PHE* 1.3 78.6 - - - +
92G ALA* 1.3 64.8 + - - +
94G VAL* 3.0 31.0 + - + +
95G VAL* 3.2 7.3 + - - +
110G TYR* 5.5 1.8 - - - +
132G LEU* 3.7 13.5 - - + -
135G VAL* 3.5 24.0 - - + -
136G TYR* 3.3 62.4 - - + +
140G VAL* 3.7 13.5 - - + -
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Residues in contact with ALA 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G LYS* 2.9 25.3 + - + +
89G SER* 3.6 6.3 - - - +
91G LEU* 1.3 71.4 - - - +
93G MET* 1.3 57.8 + - - +
95G VAL* 2.8 32.2 + - - +
96G ASP* 3.2 9.9 + - - +
135G VAL* 4.0 14.7 - - + +
139G LYS* 4.1 17.6 + - - +
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Residues in contact with MET 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G SER* 3.1 37.7 - - - +
62G LEU* 3.8 15.5 - - + -
63G GLN* 2.7 43.3 - - + +
89G SER 3.0 10.5 + - - +
90G PHE* 3.5 9.2 - - - +
92G ALA* 1.3 79.8 - - - +
94G VAL* 1.3 65.3 + - - +
95G VAL 3.0 0.3 + - - -
96G ASP* 3.0 19.3 + - + +
97G ILE* 2.9 34.3 + - + +
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Residues in contact with VAL 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ILE* 4.1 16.8 - - + -
62G LEU* 3.8 16.2 - - + -
82G THR* 3.7 30.7 - - + -
85G THR* 5.7 0.4 - - - +
90G PHE* 2.9 37.7 + - + +
91G LEU* 3.0 20.2 + - + +
93G MET* 1.3 75.5 - - - +
95G VAL* 1.3 52.1 + - + +
97G ILE* 3.2 11.5 + - + +
98G VAL* 2.7 45.9 + - + +
110G TYR* 4.7 4.5 - - - +
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Residues in contact with VAL 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G LEU* 3.6 9.6 - - + +
92G ALA* 2.8 15.2 + - - +
94G VAL* 1.3 74.7 - - + +
96G ASP* 1.3 71.4 + - - +
98G VAL* 2.7 21.6 + - + +
99G GLN* 2.9 29.5 + - - +
110G TYR* 6.1 0.4 - - + -
139G LYS* 3.5 37.5 - - + +
140G VAL* 3.7 30.3 - - + -
143G VAL* 4.3 12.1 - - + -
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Residues in contact with ASP 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G ALA 3.5 6.6 - - - +
93G MET* 3.0 18.5 + - + +
95G VAL* 1.3 75.8 - - - +
97G ILE* 1.3 64.2 + - + +
99G GLN* 3.2 12.9 + - - +
100G GLU* 2.9 23.8 + - - +
139G LYS* 3.2 25.4 + - - -
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Residues in contact with ILE 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LEU* 4.6 9.4 - - + -
10G ILE* 5.2 7.6 - - + -
62G LEU* 3.8 34.5 - - + -
66G TYR* 3.7 55.4 - - + -
93G MET* 2.9 26.2 + - + +
94G VAL* 3.2 10.3 - - + +
96G ASP* 1.3 76.5 - - + +
98G VAL* 1.3 66.1 + - + +
100G GLU* 3.2 8.7 + - - +
101G LEU* 3.0 32.4 + - + +
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Residues in contact with VAL 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G VAL* 4.4 17.9 - - + -
94G VAL* 2.7 43.4 + - + +
95G VAL* 2.7 16.0 + - - +
97G ILE* 1.3 72.8 - - + +
99G GLN* 1.3 56.8 + - - +
101G LEU* 3.2 12.3 + - - +
102G LYS* 2.8 32.9 + - + +
108G LEU* 5.1 0.7 - - + -
110G TYR* 3.5 46.2 - - + -
143G VAL* 4.1 15.7 - - + -
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Residues in contact with GLN 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G VAL* 2.9 29.6 + - + +
96G ASP* 3.6 14.1 - - - +
98G VAL* 1.3 72.9 - - - +
100G GLU* 1.3 66.0 + - - +
102G LYS* 3.0 16.9 + - + +
103G GLN* 3.0 29.6 + - - +
139G LYS* 5.8 0.2 + - - -
143G VAL* 4.0 24.8 - - + +
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Residues in contact with GLU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G TYR* 3.3 33.7 + - - +
70G LYS* 3.9 18.3 + - - +
75G ASN* 3.9 0.2 + - - -
96G ASP 2.9 13.2 + - - +
97G ILE* 3.6 9.0 - - - +
99G GLN* 1.3 77.0 - - - +
101G LEU* 1.3 59.7 + - - +
103G GLN* 3.4 7.9 + - - +
104G GLN* 3.1 42.5 + - + +
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Residues in contact with LEU 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LEU* 4.2 5.8 - - + -
66G TYR* 3.4 22.4 - - + +
75G ASN 3.4 24.5 - - - +
76G GLN* 4.9 1.8 - - - -
77G TYR* 3.9 27.1 - - + +
80G VAL* 4.1 21.1 - - + -
97G ILE* 3.0 31.2 + - + +
98G VAL* 3.4 7.4 - - - +
99G GLN 3.0 0.6 - - - -
100G GLU* 1.3 74.4 - - - +
102G LYS* 1.3 54.4 + - - +
103G GLN 3.1 1.8 - - - -
104G GLN* 3.2 12.8 + - - +
105G ASN* 2.7 38.2 + - - +
108G LEU* 3.8 13.9 - - + -
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Residues in contact with LYS 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G VAL* 2.8 17.7 + - + +
99G GLN* 3.0 9.8 + - + +
101G LEU* 1.3 75.6 - - - +
103G GLN* 1.3 69.7 + - - +
105G ASN 3.0 22.9 - - - +
106G PRO* 3.2 14.1 + - + +
108G LEU* 3.0 39.6 + - + +
110G TYR* 4.5 4.3 - - - -
143G VAL* 3.7 35.4 - - + -
145G ASP* 2.4 39.0 + - - -
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Residues in contact with GLN 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G GLN* 3.0 24.1 + - - +
100G GLU* 3.5 12.3 - - - +
102G LYS* 1.3 88.1 + - - +
104G GLN* 1.3 66.9 + - + +
105G ASN 3.4 0.2 + - - -
106G PRO* 3.9 10.4 - - - +
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Residues in contact with GLN 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LYS* 3.8 7.9 + - - +
75G ASN* 3.3 43.1 + - - +
76G GLN* 4.6 10.1 - - - +
100G GLU* 3.1 33.9 - - + +
101G LEU* 3.2 12.4 + - - +
103G GLN* 1.3 78.6 - - + +
105G ASN* 1.3 60.5 + - + +
106G PRO* 3.5 6.4 - - - +
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Residues in contact with ASN 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G TYR 3.2 25.5 - - - +
78G ASP* 4.1 10.0 - - - +
101G LEU 2.7 13.3 + - - +
102G LYS* 3.0 13.3 - - - +
104G GLN* 1.3 74.6 - - + +
106G PRO* 1.3 66.5 - - - +
107G ARG* 2.7 31.0 - - - +
108G LEU* 3.2 28.6 + - + +
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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
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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