Contacts of the helix formed by residues 64 - 76 (chain G) in PDB entry 5U07
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 ARG 64 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62G THR* 3.4 2.4 - - - -
63G ARG* 1.3 90.3 - - - +
65G ILE* 1.3 62.8 + - - +
66G ILE 3.4 2.9 - - - +
67G SER* 3.8 15.6 + - - +
68G GLU 3.7 7.1 + - - -
110G ALA 5.7 2.7 - - - +
111G PRO 5.1 1.6 - - - +
112G ALA* 4.4 22.2 - - + +
208H ASP* 2.3 34.9 + - - +
210H ILE* 3.3 45.6 + - + +
211H PRO 5.4 0.7 - - - -
212H LYS* 3.5 24.8 - - - +
214H ASN* 4.8 3.8 - - - +
215H ASP* 2.8 42.8 + - - +
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Residues in contact with ILE 65 (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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60G VAL* 5.6 0.4 - - + -
62G THR* 4.3 15.1 + - - +
63G ARG 3.6 1.8 + - - -
64G ARG* 1.3 75.3 - - - +
66G ILE* 1.3 69.9 + - - +
68G GLU* 3.0 6.3 + - + +
69G ILE* 2.9 40.5 + - + +
91G VAL* 4.0 19.5 - - + -
113G THR* 4.1 6.0 - - + +
117G PHE* 3.9 36.1 - - + -
119G LEU* 4.4 17.7 - - + -
124G ILE* 3.7 35.9 - - + -
127G LEU* 5.6 3.4 - - + -
210H ILE* 5.5 0.2 - - - -
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Residues in contact with ILE 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ARG 3.4 0.4 - - - -
65G ILE* 1.3 79.7 - - + +
67G SER* 1.3 57.3 - - - +
69G ILE* 3.5 2.4 + - - -
70G ALA* 2.9 28.3 + - + +
84G ASP* 4.2 9.0 - - - +
87G ALA* 3.5 27.9 - - + +
88G ARG* 4.3 7.9 - - + +
91G VAL* 3.5 42.6 - - + -
102G LEU* 4.0 18.4 - - + -
110G ALA* 3.6 19.1 - - + -
111G PRO* 3.5 32.5 - - + +
113G THR* 4.4 3.6 - - + -
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Residues in contact with SER 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ARG* 3.8 23.0 + - - +
65G ILE 3.2 0.6 - - - -
66G ILE* 1.3 80.3 - - - +
68G GLU* 1.3 56.4 + - - +
70G ALA* 3.3 6.2 + - - +
71G LYS* 2.9 25.6 + - - +
74G ARG* 4.3 4.2 + - - -
109G GLU* 5.9 2.1 - - - +
110G ALA* 4.0 22.4 + - - +
111G PRO 5.4 0.4 + - - -
210H ILE* 5.5 2.1 - - - +
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Residues in contact with GLU 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ARG 3.7 1.9 + - - +
65G ILE* 3.0 11.8 + - + +
67G SER* 1.3 75.3 - - - +
69G ILE* 1.3 63.1 + - - +
71G LYS* 2.8 40.9 + - - +
72G ARG* 2.3 52.2 + - - +
124G ILE* 3.0 36.2 - - + +
210H ILE* 4.2 29.8 - - + +
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Residues in contact with ILE 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ILE* 2.9 39.7 + - + +
66G ILE* 3.9 4.0 - - - +
68G GLU* 1.3 77.9 - - - +
70G ALA* 1.3 58.0 + - - +
72G ARG* 3.2 4.5 + - - +
73G LEU* 2.9 43.3 + - + +
87G ALA* 4.1 17.7 - - + +
90G VAL* 4.0 30.3 - - + -
91G VAL* 5.7 2.0 - - + -
124G ILE* 4.1 17.0 - - + +
127G LEU* 4.2 18.2 - - + -
128G ALA* 4.4 14.1 - - - -
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Residues in contact with ALA 70 (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 ILE* 2.9 19.9 + - + +
67G SER* 3.4 9.6 - - - +
68G GLU 3.1 0.2 - - - -
69G ILE* 1.3 76.4 - - - +
71G LYS* 1.3 56.0 + - - +
73G LEU* 3.5 0.8 + - - -
74G ARG* 2.9 51.5 + - - +
83G ALA* 3.8 27.7 - - - +
84G ASP* 4.6 7.2 - - + +
87G ALA* 4.1 3.3 - - + +
110G ALA* 5.6 2.0 - - + -
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Residues in contact with LYS 71 (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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67G SER 2.9 10.5 + - - +
68G GLU* 2.8 37.9 + - - +
70G ALA* 1.3 78.4 - - - +
72G ARG* 1.3 69.4 + - - +
74G ARG* 2.9 39.9 - - + +
75G GLU* 3.0 10.7 + - + +
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Residues in contact with ARG 72 (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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68G GLU* 2.3 50.5 + - - +
69G ILE* 3.2 5.4 + - - +
71G LYS* 1.3 85.6 - - - +
73G LEU* 1.3 62.8 + - - +
75G GLU* 3.0 11.6 + - - +
76G ARG* 3.0 26.9 + - - +
121G VAL* 3.1 38.6 + - - +
122G PRO* 5.0 0.2 - - - +
124G ILE* 3.5 11.5 - - - +
125G ASP* 3.0 47.4 - - - +
128G ALA* 4.1 13.5 - - + -
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Residues in contact with LEU 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 ILE* 2.9 30.5 + - + +
70G ALA 4.1 2.9 - - - +
72G ARG* 1.3 76.1 - - - +
74G ARG* 1.3 62.3 + - - +
76G ARG* 3.0 30.8 + - - +
78G TRP* 3.3 41.8 + - + +
83G ALA* 4.2 23.6 - - + +
86G GLY 4.7 1.8 - - - -
87G ALA 4.5 6.1 - - - +
128G ALA* 3.2 30.5 - - + +
131G ALA* 3.9 21.5 - - + -
132G ASP* 4.4 9.0 - - + +
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Residues in contact with ARG 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G SER* 4.3 4.6 + - - -
70G ALA* 2.9 35.1 + - - +
71G LYS* 2.9 52.2 - - + +
73G LEU* 1.3 77.0 - - - +
75G GLU* 1.3 61.6 + - + +
77G GLY* 3.3 10.9 + - - -
78G TRP* 3.8 20.4 - - - +
80G ALA* 4.7 27.9 + - - +
83G ALA* 4.2 6.5 - - + +
84G ASP* 5.4 1.8 - - - +
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Residues in contact with GLU 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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71G LYS* 3.0 16.0 + - + +
72G ARG* 3.0 13.2 + - - +
74G ARG* 1.3 79.6 - - + +
76G ARG* 1.3 70.4 + - - +
77G GLY* 3.2 2.0 + - - -
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Residues in contact with ARG 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ARG* 3.0 14.4 + - + +
73G LEU* 3.0 30.0 + - - +
75G GLU* 1.3 85.5 - - - +
77G GLY* 1.3 55.0 - - - +
78G TRP* 3.6 10.9 - - + +
125G ASP* 3.0 27.4 + - - -
128G ALA* 3.9 15.4 - - - +
129G ALA* 3.6 32.6 - - - +
132G ASP* 3.9 23.2 + - - +
135G ARG* 5.7 1.7 + - - -
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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