Contacts of the helix formed by residues 64 - 76 (chain I) in PDB entry 5U0A
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E ASP* 2.8 28.7 + - - +
210E ILE* 2.7 47.0 + - + +
211E PRO* 4.6 3.6 - - - +
212E LYS* 3.7 43.4 - - - +
215E ASP* 4.2 5.5 + - - -
217E GLY* 4.7 8.3 + - - -
62I THR* 3.0 15.4 + - - +
63I ARG* 1.3 94.8 - - + +
65I ILE* 1.3 63.6 + - - +
66I ILE 3.4 2.9 - - - +
67I SER* 4.2 15.1 - - - +
68I GLU* 3.7 17.0 + - - +
110I ALA 5.9 3.1 - - - +
111I PRO 5.4 0.9 - - - -
112I ALA* 4.3 18.5 - - + +
24M A 5.9 2.4 - - - -
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Residues in contact with ILE 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I THR* 4.2 14.7 - - + +
63I ARG 3.6 3.4 + - - -
64I ARG* 1.3 73.8 - - - +
66I ILE* 1.3 71.3 + - - +
68I GLU* 3.1 5.0 + - - +
69I ILE* 3.0 30.1 + - + +
90I VAL* 5.9 0.4 - - + -
91I VAL* 4.0 17.5 - - + -
113I THR* 4.0 22.6 - - + +
117I PHE* 4.1 20.0 - - + -
119I LEU* 4.2 20.2 - - + -
124I ILE* 3.9 19.5 - - + -
127I LEU* 4.0 26.5 - - + -
160I LEU* 5.1 1.6 - - + -
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Residues in contact with ILE 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I ARG* 3.4 0.6 - - - +
65I ILE* 1.3 80.6 - - + +
67I SER* 1.3 57.7 + - - +
69I ILE* 3.4 2.5 + - - -
70I ALA* 2.9 27.9 + - + +
84I ASP* 4.4 8.1 - - - +
87I ALA* 3.4 28.8 - - + +
88I ARG* 4.3 8.1 - - + +
91I VAL* 3.7 41.3 - - + -
102I LEU* 3.7 22.4 - - + -
110I ALA* 3.8 17.7 - - + -
111I PRO* 3.5 28.7 + - + +
113I THR* 4.6 2.9 - - + -
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Residues in contact with SER 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E ILE* 5.6 5.0 - - - +
64I ARG* 3.9 21.5 + - - +
65I ILE 3.3 0.4 - - - -
66I ILE* 1.3 77.6 - - - +
68I GLU* 1.3 58.3 + - - +
70I ALA* 3.1 10.9 + - - +
71I LYS* 3.0 27.8 + - - +
74I ARG* 5.4 0.2 + - - -
110I ALA* 4.2 20.7 - - - +
111I PRO 5.6 0.2 + - - -
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Residues in contact with GLU 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210E ILE* 4.2 34.0 - - + +
62I THR* 6.2 0.4 - - + -
64I ARG 3.7 10.8 + - - +
65I ILE* 3.1 8.1 + - - +
67I SER* 1.3 76.3 + - - +
69I ILE* 1.3 68.1 + - - +
71I LYS* 3.0 48.4 + - - +
72I ARG* 2.8 54.6 + - - +
124I ILE* 3.5 13.2 - - + -
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Residues in contact with ILE 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I ILE* 3.0 30.9 + - + +
66I ILE* 3.8 4.9 - - - +
68I GLU* 1.3 75.0 - - - +
70I ALA* 1.3 57.2 + - - +
72I ARG* 3.2 8.4 + - - +
73I LEU* 2.9 35.4 + - + +
87I ALA* 3.9 20.6 - - + +
90I VAL* 3.9 33.4 - - + -
91I VAL* 5.7 1.1 - - + -
124I ILE* 3.9 20.6 - - + +
127I LEU* 4.1 19.7 - - + -
128I ALA* 4.2 20.4 - - - -
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Residues in contact with ALA 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ILE* 2.9 15.4 + - + +
67I SER* 3.2 16.4 - - - +
69I ILE* 1.3 78.2 - - - +
71I LYS* 1.3 55.4 + - - +
74I ARG* 2.9 48.7 + - - +
83I ALA* 3.8 26.9 - - - +
84I ASP* 4.7 6.1 - - + +
87I ALA* 4.2 1.7 - - + +
110I ALA* 5.8 2.5 - - + -
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Residues in contact with LYS 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I SER* 3.0 12.0 + - - +
68I GLU* 3.1 48.4 + - - +
70I ALA* 1.3 75.8 - - - +
72I ARG* 1.3 61.3 + - + +
74I ARG* 3.3 15.8 + - - +
75I GLU* 2.9 30.6 + - - +
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Residues in contact with ARG 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I GLU* 2.8 56.2 + - - +
69I ILE* 3.9 3.3 - - - +
71I LYS* 1.3 78.9 - - + +
73I LEU* 1.3 63.6 + - - +
75I GLU* 3.0 21.6 - - + +
76I ARG* 3.0 26.6 + - - +
121I VAL* 4.3 14.1 + - - +
124I ILE* 3.0 37.4 - - - +
125I ASP* 3.8 34.0 - - - +
128I ALA* 3.7 17.9 - - + -
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Residues in contact with LEU 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I ILE* 2.9 26.0 + - + +
72I ARG* 1.3 76.1 - - - +
74I ARG* 1.3 62.1 + - - +
76I ARG* 3.1 23.7 + - - -
78I TRP* 3.2 53.4 + - + +
83I ALA* 3.9 35.0 - - + +
86I GLY 4.3 2.0 - - - -
87I ALA 4.2 8.5 - - - +
128I ALA* 3.2 29.8 - - + +
131I ALA* 4.1 18.8 - - + -
132I ASP* 4.2 3.4 - - + +
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Residues in contact with ARG 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I ALA* 2.9 42.0 + - - +
71I LYS* 3.6 17.4 - - - +
73I LEU* 1.3 78.3 - - - +
75I GLU* 1.3 59.3 + - - +
77I GLY* 3.4 10.2 + - - -
78I TRP 4.0 19.6 - - - +
80I ALA* 3.8 39.2 + - - +
83I ALA* 4.0 5.2 - - + +
84I ASP* 5.3 2.0 - - - +
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Residues in contact with GLU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I LYS 2.9 17.1 + - - +
72I ARG* 3.0 34.3 - - + +
74I ARG* 1.3 75.7 - - - +
76I ARG* 1.3 69.6 + - - +
77I GLY 3.2 2.3 + - - -
125I ASP* 4.9 4.5 - - - +
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Residues in contact with ARG 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ARG 3.0 17.8 + - - +
73I LEU* 3.1 20.0 + - - +
75I GLU* 1.3 86.9 + - - +
77I GLY* 1.3 58.1 + - - +
78I TRP* 3.6 11.5 - - + +
125I ASP* 3.4 25.6 + - - -
128I ALA* 4.1 14.5 - - - +
129I ALA* 3.6 29.9 - - - +
132I ASP* 3.5 33.4 + - - +
135I ARG* 5.0 3.5 + - - -
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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