Contacts of the helix formed by residues 71 - 88 (chain G) in PDB entry 3UF2
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 THR 71 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G PHE* 3.8 4.7 - - - +
68G ARG* 2.9 50.1 + - + +
69G ASP 4.0 2.9 - - - +
70G ASN* 1.3 79.3 - - - +
72G PRO* 1.3 67.5 - - + +
73G ASN* 4.1 2.5 + - - +
74G ALA* 2.6 33.4 + - - +
75G ILE* 3.1 9.8 + - - +
24H ASP* 3.7 39.3 + - + +
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Residues in contact with PRO 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ASN 3.9 2.9 - - - +
71G THR* 1.3 87.3 - - - +
73G ASN* 1.3 64.4 + - - +
75G ILE* 3.5 11.6 + - + +
76G ALA* 3.1 25.2 + - - +
21H ARG* 6.5 0.9 - - - -
24H ASP* 5.5 4.0 - - + -
25H SER* 6.5 0.9 - - - -
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Residues in contact with ASN 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G SER 5.3 0.3 - - - +
21G ARG* 4.6 3.8 - - - +
22G LEU* 3.8 22.5 + - + +
25G SER* 3.0 27.1 + - - -
26G GLN* 4.2 0.4 - - - +
67G PHE* 3.7 25.9 - - + -
71G THR* 3.1 3.0 + - - +
72G PRO* 1.3 81.7 - - - +
74G ALA* 1.3 65.9 + - - +
75G ILE 3.4 0.2 - - - -
76G ALA* 3.5 9.1 + - - +
77G ILE* 3.3 26.7 + - - +
25H SER* 3.1 33.4 + - - -
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Residues in contact with ALA 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G PHE* 3.7 21.7 - - + +
68G ARG 3.2 25.8 - - - +
69G ASP* 4.5 1.6 - - - +
70G ASN 3.9 7.4 - - - +
71G THR* 2.6 23.8 + - - +
73G ASN* 1.3 70.5 - - - +
75G ILE* 1.3 64.7 + - - +
77G ILE* 3.2 7.3 + - - +
78G VAL* 3.1 22.7 + - + +
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Residues in contact with ILE 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ASN* 4.1 31.4 - - - +
71G THR 3.1 7.9 + - - +
72G PRO* 3.7 10.5 - - + +
74G ALA* 1.3 75.7 - - + +
76G ALA* 1.3 66.5 + - - +
78G VAL* 2.8 14.6 + - + +
79G GLN* 2.8 47.2 + - + +
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Residues in contact with ALA 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G SER* 4.3 24.4 + - - +
22G LEU* 3.7 18.6 - - + -
72G PRO 3.1 11.9 + - - +
73G ASN* 3.5 13.0 - - - +
74G ALA 3.3 0.4 - - - -
75G ILE* 1.3 78.2 - - - +
77G ILE* 1.3 57.9 + - - +
79G GLN* 3.4 12.5 + - - +
80G LEU* 3.0 35.8 + - + +
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Residues in contact with ILE 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU* 6.3 0.2 - - + -
22G LEU* 3.7 20.9 - - + -
61G MET* 3.7 33.0 - - + +
65G MET* 4.1 25.1 - - - +
67G PHE* 3.6 25.4 - - + -
73G ASN 3.3 14.4 - - - +
74G ALA* 3.2 7.4 + - - +
75G ILE 3.1 0.6 - - - -
76G ALA* 1.3 74.1 - - - +
78G VAL* 1.3 61.3 + - + +
80G LEU* 3.1 13.8 + - + +
81G GLN* 2.8 41.6 + - - +
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Residues in contact with VAL 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ALA 3.1 14.6 + - - +
75G ILE* 2.8 15.6 + - + +
77G ILE* 1.3 78.0 - - + +
79G GLN* 1.3 59.4 + - + +
81G GLN* 3.3 14.3 + - - +
82G GLU* 3.0 45.6 + - + +
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Residues in contact with GLN 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G HIS* 4.4 16.7 + - + +
18G SER* 5.1 9.1 + - - +
75G ILE* 2.8 39.1 + - + +
76G ALA* 3.6 12.2 - - - +
78G VAL* 1.3 74.5 - - + +
80G LEU* 1.3 59.2 + - + +
82G GLU* 3.5 17.5 - - - +
83G LEU* 2.9 26.0 + - - +
86G ARG* 4.6 2.1 + - - +
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Residues in contact with LEU 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G HIS* 4.2 27.1 - - + +
18G SER* 4.6 7.0 - - - +
19G LEU* 3.5 36.8 - - + -
22G LEU* 5.0 4.3 - - + -
61G MET* 3.8 18.1 - - + +
76G ALA* 3.0 27.5 + - + +
77G ILE* 3.1 19.3 + - + +
79G GLN* 1.3 76.9 - - + +
81G GLN* 1.3 60.0 + - - +
83G LEU* 3.3 25.9 + - + +
84G SER* 3.0 29.6 + - - -
117G VAL* 5.6 0.4 - - + -
121G PHE* 4.3 9.6 - - + -
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Residues in contact with GLN 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G GLN* 4.3 14.9 + - + +
61G MET* 4.0 25.1 - - + +
62G GLU* 2.9 48.0 + - - +
77G ILE* 2.8 34.8 + - - +
78G VAL* 3.7 15.1 - - - +
80G LEU* 1.3 73.4 - - - +
82G GLU* 1.3 60.9 + - + +
84G SER* 3.0 6.0 + - - -
85G LEU* 2.9 34.2 + - + +
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Residues in contact with GLU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G VAL* 3.0 31.2 + - + +
79G GLN* 3.5 22.2 - - - +
81G GLN* 1.3 77.4 - - + +
83G LEU* 1.3 61.6 + - - +
85G LEU* 2.9 30.0 + - + +
86G ARG* 3.3 33.3 + - - +
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Residues in contact with LEU 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G MET* 3.6 30.5 - - + +
11G ILE* 4.2 9.0 - - + -
15G HIS* 3.9 28.7 - - + +
79G GLN 2.9 15.5 + - - +
80G LEU* 3.4 14.8 - - + +
81G GLN 3.3 0.2 - - - -
82G GLU* 1.3 75.3 - - - +
84G SER* 1.3 57.5 + - - +
86G ARG* 3.3 27.9 + - - +
87G LEU* 3.1 42.4 + - + +
121G PHE* 3.6 31.0 - - + -
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Residues in contact with SER 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G PHE* 3.4 27.6 - - - -
57G VAL* 4.6 3.0 - - - +
58G GLN* 4.6 17.3 - - - -
61G MET* 3.8 9.1 - - - +
80G LEU 3.0 14.6 + - - -
81G GLN* 3.0 11.9 + - - -
83G LEU* 1.3 74.5 - - - +
85G LEU* 1.3 64.4 + - - +
88G LYS* 3.3 24.3 + - - +
121G PHE* 3.5 22.0 - - - -
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Residues in contact with LEU 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G GLN* 3.8 19.3 - - - +
81G GLN* 2.9 21.4 + - + +
82G GLU* 2.9 22.4 + - + +
84G SER* 1.3 76.6 - - - +
86G ARG* 1.3 62.2 + - + +
88G LYS* 4.0 29.2 + - - +
89G SER* 4.9 1.0 + - - -
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Residues in contact with ARG 86 (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 MET* 3.3 36.6 + - + +
15G HIS* 4.4 10.7 + - - -
79G GLN* 4.6 3.2 + - - +
82G GLU* 3.3 34.2 + - - +
83G LEU* 3.3 43.3 + - - +
84G SER 3.2 0.4 - - - -
85G LEU* 1.3 77.2 - - + +
87G LEU* 1.3 60.3 + - - +
88G LYS 3.2 2.8 + - - -
89G SER* 2.9 26.3 + - - -
90G CYS* 4.6 2.8 - - - -
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Residues in contact with LEU 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G MET* 3.8 28.3 - - + -
11G ILE* 4.0 18.8 - - + -
54G PHE* 3.3 35.9 - - + -
83G LEU* 3.1 38.4 + - + +
84G SER 3.4 0.6 + - - -
86G ARG* 1.3 73.2 - - - +
88G LYS* 1.3 58.9 + - - +
89G SER 3.1 3.6 - - - -
90G CYS* 2.8 29.7 + - + +
91G PHE* 3.1 21.2 - - + -
121G PHE* 4.6 4.7 - - + -
124G THR* 4.9 3.6 - - + -
128G LEU* 4.2 23.1 - - + -
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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
----------------------------------------------------------
54G PHE* 3.9 17.5 - - + -
55G LEU* 5.3 10.8 - - + -
58G GLN* 4.3 18.7 + - - +
84G SER 3.3 12.9 + - - +
85G LEU* 4.0 37.3 - - - +
86G ARG 3.2 1.0 - - - -
87G LEU* 1.3 77.0 - - - +
89G SER* 1.3 57.0 + - - +
90G CYS 3.1 0.2 - - - -
91G PHE* 3.0 28.9 + - - +
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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
------------------------------------------------------------
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