Contacts of the helix formed by residues 62 - 73 (chain C) in PDB entry 3H1J
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 LEU 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C THR* 3.6 33.4 - - + -
59C ASP* 2.7 13.8 + - + +
61C SER* 1.3 90.7 + - - +
63C ALA* 1.3 64.9 + - - +
64C PHE 3.4 2.0 - - - -
65C SER* 3.1 13.4 + - - +
66C SER* 2.8 24.8 + - - -
59P ASP* 4.1 23.3 - - - +
61P SER* 5.2 1.1 - - - +
62P LEU* 4.2 17.5 - - + -
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 3.5 25.1 - - - +
57C THR 3.4 11.6 + - - +
59C ASP 2.6 19.8 + - - +
60C THR 4.1 1.1 + - - +
62C LEU* 1.3 70.5 - - - +
64C PHE* 1.3 65.4 + - - +
66C SER* 2.7 21.4 + - - -
67C VAL* 3.1 12.9 - - - +
134C LEU 3.7 6.7 - - - +
135C PRO 4.1 0.2 - - - -
136C TRP* 4.0 8.1 - - + -
176C LEU* 3.6 15.0 - - + -
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Residues in contact with PHE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR 4.9 5.1 + - - +
62C LEU 3.4 0.6 - - - -
63C ALA* 1.3 79.0 - - - +
65C SER* 1.3 62.9 + - - +
67C VAL* 3.3 2.0 + - - +
68C ALA* 3.2 15.5 + - + +
135C PRO 3.2 25.2 + - - +
136C TRP* 3.8 17.8 - - + +
137C GLY* 4.2 0.7 - - - -
256C ASN 4.1 4.9 - - - -
257C PHE* 3.4 29.4 - - - -
258C THR 4.2 0.4 - - - -
259C PRO* 3.5 40.2 - - + -
2011C GOL 3.3 40.1 + - - -
45D TYR* 3.5 31.4 - + - -
115D TYR* 4.7 12.6 - + - -
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C SER 4.1 4.9 + - - -
62C LEU* 3.1 27.9 + - - +
64C PHE* 1.3 77.0 - - - +
66C SER* 1.3 52.1 + - - +
68C ALA* 3.1 2.1 + - - +
69C HIS* 2.7 35.7 + - - +
45D TYR* 3.7 31.7 - - - -
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Residues in contact with SER 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C HIS 3.8 16.9 - - - +
56C TYR* 3.5 8.7 - - - -
57C THR* 3.4 30.8 + - - -
62C LEU* 2.8 20.1 + - - -
63C ALA* 2.7 17.8 + - - -
65C SER* 1.3 71.8 - - - +
67C VAL* 1.3 58.5 + - - +
69C HIS* 3.2 9.0 + - - +
70C THR* 2.7 32.3 + - - -
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C TYR* 3.9 20.6 - - + +
63C ALA 3.1 16.4 - - - +
64C PHE 3.5 6.1 - - - +
66C SER* 1.3 80.9 - - - +
68C ALA* 1.3 62.1 + - - +
70C THR* 3.1 11.3 + - - -
71C CYS* 3.0 26.4 + - - -
81C ARG* 3.5 39.5 - - + +
135C PRO* 4.0 16.6 - - + -
501C HEM 4.0 19.7 - - + +
2011C GOL 4.0 6.1 - - - +
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C PHE* 3.2 10.0 + - + +
65C SER 3.1 8.8 + - - +
67C VAL* 1.3 78.9 - - - +
69C HIS* 1.3 51.1 + - - +
71C CYS* 3.1 2.6 + - - +
72C ARG* 2.7 41.7 + - - +
2011C GOL 3.9 9.9 + - - +
45D TYR* 3.5 28.9 - - + -
115D TYR* 3.2 27.8 - - + +
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Residues in contact with HIS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C HIS* 4.5 13.6 + + + +
65C SER 2.7 19.4 + - - +
66C SER* 3.5 9.0 + - - +
68C ALA* 1.3 71.1 - - - +
70C THR* 1.3 64.7 + - - +
72C ARG* 4.3 1.3 - - - +
73C ASN* 2.6 65.5 + - + +
74C VAL* 3.4 26.6 + - + +
45D TYR* 5.3 1.3 - - - -
65E SER* 3.8 5.6 + - - -
67E ASP* 3.1 28.1 + - - -
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 4.0 26.5 + - + -
55C HIS* 3.3 29.8 + - + +
56C TYR* 5.2 0.5 - - - -
66C SER 2.7 22.0 + - - -
67C VAL* 3.1 14.3 + - - -
69C HIS* 1.3 74.6 + - - +
71C CYS* 1.3 64.0 + - - +
74C VAL* 3.1 33.8 + - + +
77C GLY* 3.3 25.1 - - - +
81C ARG* 5.1 1.1 - - + -
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Residues in contact with CYS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C VAL 3.0 14.5 + - - +
68C ALA 3.6 6.3 - - - +
70C THR* 1.3 84.5 - - - +
72C ARG* 1.3 63.3 + - + +
74C VAL 4.5 2.4 - - - +
78C TRP* 3.7 38.7 + - + +
81C ARG* 3.5 49.4 - - - -
82C ASN* 5.7 1.3 - - - -
2011C GOL 4.2 9.4 - - - +
115D TYR* 4.9 0.9 - - + +
197D GLU* 5.0 5.3 - - - +
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Residues in contact with ARG 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ALA 2.7 21.8 + - - +
69C HIS* 4.2 0.9 - - - +
71C CYS* 1.3 78.3 - - + +
73C ASN* 1.3 70.3 + - - +
74C VAL 5.1 0.2 - - - -
45D TYR* 3.3 45.6 + - - +
46D VAL* 4.4 5.7 - - - +
49D ARG* 5.5 0.2 + - - -
50D ASN* 5.2 7.6 - - - +
114D SER* 3.8 11.5 + - - +
115D TYR* 2.7 47.0 + - - +
193D ALA 2.6 32.1 + - - -
194D ALA* 3.9 3.2 - - - +
196D PRO* 4.0 21.2 - - + +
197D GLU* 6.2 0.2 - - - +
66E ALA* 4.9 4.3 - - - +
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Residues in contact with ASN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C HIS* 2.6 49.4 + - + +
72C ARG* 1.3 85.4 - - - +
74C VAL* 1.3 64.7 + - - +
75C GLN* 3.3 5.7 + - - +
49D ARG* 3.0 27.4 + - - -
50D ASN* 5.3 0.7 + - - +
90D TYR* 3.7 15.4 + - - -
65E SER* 3.3 2.9 - - - -
66E ALA* 3.1 24.5 + - - +
67E ASP* 3.4 32.6 + - - +
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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