Contacts of the helix formed by residues 66 - 80 (chain G) in PDB entry 5IC4
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 GLY 66 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53G LYS* 5.0 4.0 - - - +
65G SER* 1.3 73.2 - - - +
67G THR* 1.3 61.9 + - - +
68G ASP* 3.2 4.4 - - - +
69G VAL* 3.2 29.8 + - - +
70G ASP* 3.4 2.3 + - - -
207H ARG* 4.5 2.2 - - - -
208H ASN 3.9 8.1 - - - -
209H SER 3.3 18.3 + - - -
212H GLY* 3.4 15.2 - - - -
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Residues in contact with THR 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ASN* 2.5 33.5 + - - +
53G LYS* 3.6 29.2 - - + -
64G ARG* 2.9 52.4 + - - +
65G SER 3.4 0.6 + - - -
66G GLY* 1.3 75.1 - - - +
68G ASP* 1.3 63.4 + - - +
70G ASP* 3.2 12.3 + - - +
71G ALA* 2.8 23.4 + - - +
119G LEU* 3.8 6.6 - - - +
207H ARG* 4.3 2.8 - - - +
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Residues in contact with ASP 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ASN* 2.9 24.9 + - - +
53G LYS* 3.0 38.4 + - - +
66G GLY* 3.2 2.1 - - - +
67G THR* 1.3 75.8 - - - +
69G VAL* 1.3 63.2 + - + +
71G ALA* 3.9 2.0 - - - +
72G ALA* 3.0 31.9 + - - +
89G ASN* 4.6 2.3 - - - +
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Residues in contact with VAL 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G GLY* 3.3 18.4 - - - +
68G ASP* 1.3 78.7 - - + +
70G ASP* 1.3 62.0 + - - +
72G ALA* 4.0 3.9 - - - +
73G ASN* 3.0 27.8 + - + +
209H SER 5.5 0.2 - - - +
210H LYS* 3.6 20.4 - - - +
211H ASP 3.4 23.8 - - - +
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Residues in contact with ASP 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ARG* 5.0 2.8 + - - -
66G GLY 3.4 6.6 + - - +
67G THR* 3.2 15.2 + - - +
68G ASP 3.2 0.4 - - - -
69G VAL* 1.3 78.2 - - - +
71G ALA* 1.3 57.1 - - - +
73G ASN* 3.1 4.7 + - - +
74G LEU* 2.9 35.6 + - - +
119G LEU* 4.2 13.1 - - + +
161G GLN* 4.7 1.4 - - - +
207H ARG* 5.0 1.0 - - - +
211H ASP 4.5 1.7 - - - +
212H GLY* 3.5 5.9 - - - -
213H SER* 2.6 52.0 + - - +
216H ILE* 3.6 23.8 - - + +
217H GLN* 4.4 3.6 + - - +
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Residues in contact with ALA 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ILE* 4.2 2.1 - - + +
51G ASN* 3.6 32.3 - - + +
67G THR 2.8 19.1 + - - +
68G ASP* 3.9 4.5 - - - +
70G ASP* 1.3 73.6 - - - +
72G ALA* 1.3 58.5 + - - +
74G LEU* 3.9 5.2 - - - +
75G ARG* 3.2 25.8 + - - +
87G ASN* 3.4 20.5 + - - +
89G ASN* 5.2 1.6 - - - +
119G LEU* 4.0 9.8 - - + +
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Residues in contact with ALA 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASP 3.0 18.4 + - - +
69G VAL* 4.0 4.9 - - - +
71G ALA* 1.3 75.1 - - - +
73G ASN* 1.3 63.9 + - - +
75G ARG* 3.3 10.7 + - - +
76G GLU* 3.2 23.2 + - - +
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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
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69G VAL* 3.0 22.7 + - + +
70G ASP* 3.6 6.0 + - - +
72G ALA* 1.3 75.9 - - - +
74G LEU* 1.3 56.5 + - - +
76G GLU* 3.6 4.3 + - - +
77G THR* 2.7 40.2 + - - -
216H ILE* 4.5 2.8 + - + +
217H GLN* 4.5 15.4 + - - +
220H CYS* 3.4 30.1 - - - +
221H ALA 5.3 0.2 - - - +
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Residues in contact with LEU 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ILE* 3.7 18.2 - - + -
70G ASP 2.9 20.6 + - - +
71G ALA* 3.9 2.2 - - - +
73G ASN* 1.3 74.5 - - - +
75G ARG* 1.3 64.6 + - - +
77G THR* 3.3 0.8 + - - -
78G PHE* 3.0 53.3 + - + +
117G VAL* 3.6 31.0 - - + -
119G LEU* 3.7 19.3 - - + -
216H ILE* 3.7 27.6 - - + -
219H LEU* 4.5 10.1 - - + -
220H CYS* 3.8 17.0 - - - -
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Residues in contact with ARG 75 (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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49G ILE* 3.9 7.8 - - - +
71G ALA 3.2 15.9 + - - +
72G ALA* 3.5 11.0 - - - +
73G ASN 3.3 0.2 - - - -
74G LEU* 1.3 77.8 - - - +
76G GLU* 1.3 58.2 + - - +
79G ARG* 3.1 32.3 + - + +
85G VAL* 4.0 22.6 + - + +
86G ARG* 5.4 0.2 - - - +
87G ASN* 2.8 43.2 + - - +
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Residues in contact with GLU 76 (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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72G ALA 3.2 12.2 + - - +
73G ASN* 4.1 6.3 - - - +
75G ARG* 1.3 78.3 - - - +
77G THR* 1.3 61.8 + - - +
79G ARG* 3.0 37.2 + - - +
80G ASN* 2.5 54.5 + - - +
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Residues in contact with THR 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G ASN* 2.7 25.8 + - - -
74G LEU* 3.3 4.5 + - - -
76G GLU* 1.3 77.5 - - - +
78G PHE* 1.3 62.9 + - + +
80G ASN* 3.4 17.4 + - - +
81G LEU* 3.4 15.8 + - + +
220H CYS* 3.4 28.5 + - - +
223H LEU* 3.7 42.6 - - + -
224H LYS* 4.8 5.9 - - + +
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Residues in contact with PHE 78 (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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47G CYS* 3.8 19.1 - - - -
74G LEU* 3.0 50.2 + - + +
77G THR* 1.3 76.7 - - + +
79G ARG* 1.3 63.7 + - - +
80G ASN 3.2 0.9 - - - -
81G LEU* 3.2 24.5 + - + -
83G TYR* 3.0 52.2 + + + +
85G VAL* 3.9 17.3 - - + -
115G VAL* 4.0 21.3 - - + -
117G VAL* 4.6 2.0 - - + -
157G LEU* 5.9 1.1 - - + -
159G ILE* 3.9 25.6 - - + -
219H LEU* 5.3 0.2 - - + -
223H LEU* 3.9 20.2 - - + -
232H PHE* 6.2 2.2 - + - -
275H PHE* 5.2 6.3 - + - -
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Residues in contact with ARG 79 (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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75G ARG* 3.1 23.4 + - + +
76G GLU* 3.0 38.8 + - - +
77G THR 3.3 0.2 - - - -
78G PHE* 1.3 77.3 - - - +
80G ASN* 1.3 70.3 + - - +
82G LYS* 3.2 22.9 + - - +
83G TYR 4.4 9.5 - - - +
85G VAL* 4.0 4.6 - - + +
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Residues in contact with ASN 80 (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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76G GLU* 2.5 51.5 + - - +
77G THR* 3.6 9.8 - - - +
79G ARG* 1.3 87.4 + - - +
81G LEU* 1.3 61.7 + - + +
82G LYS* 3.2 12.8 + - - +
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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