Contacts of the helix formed by residues 58 - 70 (chain H) in PDB entry 1R4N
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 58 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57H GLY* 1.3 67.2 - - - -
59H LEU* 1.3 64.3 + - - +
60H GLY 3.4 0.3 + - - -
61H CYS* 3.4 5.9 + - - +
62H GLU* 3.2 21.1 + - - +
90H ARG* 4.4 11.9 - - - +
91H GLN* 3.1 22.7 - - - +
296H ASN* 3.6 28.5 - - - -
176L GLY* 4.2 4.3 - - - -
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Residues in contact with LEU 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H GLY 2.7 7.3 + - - +
58H GLY* 1.3 69.8 - - - -
60H GLY* 1.3 53.5 + - - +
62H GLU* 3.1 3.5 + - - +
63H LEU* 2.5 46.0 + - + +
143H CYS 5.5 0.7 - - - +
144H GLY* 3.5 28.5 - - - -
180H GLY* 3.9 20.9 - - - +
181H GLY* 4.4 3.4 - - - +
182H THR* 4.7 0.7 - - - +
296H ASN* 3.8 21.0 - - - +
299H ILE* 3.9 14.6 - - + -
300H ALA* 3.8 34.3 - - + +
303H CYS* 5.8 0.4 - - - -
175L GLY 4.4 0.7 - - - +
176L GLY* 3.2 29.8 + - - +
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Residues in contact with GLY 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H VAL* 4.5 3.8 - - - -
54H ILE 5.5 0.4 - - - -
55H GLY 3.4 26.5 - - - -
56H ALA* 3.7 7.9 - - - -
57H GLY 3.3 6.7 + - - +
59H LEU* 1.3 79.0 - - - +
61H CYS* 1.3 65.3 + - - +
63H LEU* 2.8 8.2 + - - +
64H LEU* 2.7 29.5 + - - +
144H GLY* 5.0 1.8 + - - -
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Residues in contact with CYS 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H ALA* 4.2 5.9 - - - +
57H GLY* 4.0 16.5 - - - +
58H GLY 3.4 6.0 + - - +
59H LEU 3.3 0.4 - - - -
60H GLY* 1.3 74.5 - - - +
62H GLU* 1.3 65.3 + - - +
64H LEU* 3.0 12.0 + - - +
65H LYS 3.0 9.9 + - - -
91H GLN* 3.8 30.7 - - - -
92H PHE* 3.8 23.0 - - + -
93H LEU* 3.7 35.7 - - + +
94H PHE* 4.3 8.5 - - - -
107H ALA* 5.7 0.7 - - - -
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Residues in contact with GLU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 3.7 2.9 - - - +
47G LYS* 2.9 30.6 + - - -
48G ASN* 4.6 1.2 - - - +
495G ALA* 5.6 1.8 - - + +
58H GLY 3.2 9.4 + - - +
59H LEU* 3.1 4.8 + - - +
61H CYS* 1.3 78.8 - - - +
63H LEU* 1.3 64.3 + - - +
65H LYS* 3.2 14.2 + - - +
66H ASN* 3.0 36.1 + - - +
90H ARG 4.6 6.1 - - - +
92H PHE* 3.6 20.8 - - - -
293H ALA* 5.0 3.6 - - - +
296H ASN* 4.7 4.7 - - - +
297H ALA* 3.6 38.2 + - - +
300H ALA* 3.5 17.7 - - + -
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Residues in contact with LEU 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H VAL* 4.3 17.3 - - + -
54H ILE 5.6 0.2 - - - +
59H LEU* 2.5 28.5 + - + +
60H GLY* 2.8 11.4 + - - +
62H GLU* 1.3 72.6 - - - +
64H LEU* 1.3 57.6 + - - +
66H ASN* 3.2 4.8 + - - +
67H LEU* 2.8 40.1 + - + +
142H VAL* 3.9 30.5 - - + -
143H CYS 4.0 19.7 - - - +
300H ALA* 3.7 28.7 - - + +
303H CYS* 4.3 10.5 - - + -
304H ALA* 4.1 16.2 - - - +
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Residues in contact with LEU 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H VAL* 4.1 11.7 - - + -
56H ALA* 5.3 0.4 - - + -
60H GLY 2.7 20.8 + - - +
61H CYS* 3.4 7.0 - - - +
63H LEU* 1.3 71.5 - - - +
65H LYS* 1.3 63.6 + - - +
67H LEU* 3.4 3.8 + - - +
68H ALA* 2.9 25.8 + - - +
75H ILE* 3.6 25.4 - - + +
77H VAL* 3.3 39.0 - - + -
93H LEU* 4.2 7.0 - - + -
107H ALA* 4.0 27.8 - - + -
111H LEU* 3.1 24.0 - - + +
120H VAL* 4.5 8.1 - - + -
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Residues in contact with LYS 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 3.1 20.4 + - - +
47G LYS* 3.7 4.5 - - - +
74G PHE* 3.4 53.4 - - + -
491G HIS* 2.6 30.8 + - - +
495G ALA* 4.1 3.2 - - - +
61H CYS 3.0 10.8 + - - +
62H GLU* 3.2 30.8 + - - +
64H LEU* 1.3 79.9 - - - +
66H ASN* 1.3 84.9 + - - +
68H ALA* 3.0 12.0 + - - +
69H LEU* 3.1 13.9 + - + +
92H PHE* 3.9 13.0 - - + -
111H LEU* 3.6 9.3 - - + +
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Residues in contact with ASN 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491G HIS* 3.3 15.4 - - - +
492G THR* 4.0 5.6 - - + +
495G ALA* 3.7 6.8 - - - +
62H GLU* 3.0 24.5 + - - +
63H LEU* 3.6 2.4 - - - +
65H LYS* 1.3 107.7 + - - +
67H LEU* 1.3 62.0 + - - +
69H LEU* 3.3 2.3 + - - +
70H SER* 2.7 28.8 + - - -
300H ALA* 3.6 8.3 + - - +
301H ALA* 3.4 33.6 - - - +
304H ALA* 3.4 20.6 - - + -
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Residues in contact with LEU 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H VAL* 4.2 8.5 - - + -
53H VAL* 3.6 31.4 - - + -
63H LEU* 2.8 32.1 + - + +
64H LEU* 3.8 3.4 - - - +
66H ASN* 1.3 72.2 - - - +
68H ALA* 1.3 63.1 + - - +
70H SER* 3.1 13.1 + - - -
72H PHE* 3.3 42.3 + - + -
75H ILE* 4.2 15.9 - - + -
142H VAL* 4.1 13.7 - - + -
304H ALA* 4.7 8.5 - - - +
307H VAL* 3.8 33.7 - - + -
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Residues in contact with ALA 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H TRP* 3.4 21.3 - - - -
64H LEU 2.9 18.2 + - - +
65H LYS 3.3 4.9 - - - +
67H LEU* 1.3 78.8 - - - +
69H LEU* 1.3 58.8 + - + +
70H SER 3.5 0.2 + - - -
71H GLY 3.7 1.9 + - - -
72H PHE 3.7 15.4 - - - +
75H ILE* 4.3 4.0 - - + +
111H LEU* 3.6 26.2 - - + -
115H VAL* 4.1 17.2 - - + +
118H CYS* 4.2 9.6 - - - -
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Residues in contact with LEU 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ALA 5.4 2.2 - - - +
71G GLY 4.1 21.3 - - - +
72G ASN* 4.2 4.4 - - - +
73G ASN 4.1 9.6 - - - +
74G PHE* 3.8 26.5 - - + +
491G HIS* 3.5 52.9 + - + +
16H ARG* 5.9 0.7 - - - +
17H TRP* 3.6 15.3 - - + -
20H VAL* 4.1 7.1 - - - +
65H LYS* 3.1 14.5 + - + +
66H ASN 3.8 2.9 - - - +
68H ALA* 1.3 76.0 - - + +
70H SER* 1.3 61.5 + - - +
71H GLY 3.3 1.6 - - - -
115H VAL* 4.0 29.8 - - + -
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Residues in contact with SER 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491G HIS* 5.3 1.4 - - - +
492G THR* 3.3 25.5 + - - +
17H TRP* 4.0 1.8 - - - -
20H VAL* 3.3 28.8 - - - +
45H LEU* 4.3 0.5 - - - +
66H ASN 2.7 20.3 + - - -
67H LEU* 3.1 9.6 + - - +
69H LEU* 1.3 80.1 - - - +
71H GLY* 1.3 58.5 + - - +
72H PHE* 4.0 16.2 - - - -
304H ALA 5.6 0.6 + - - -
308H PHE* 3.6 21.2 - - - -
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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