Contacts of the helix formed by residues 74 - 88 (chain C) in PDB entry 1PV2
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 HIS 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C GLY 3.6 0.2 + - - -
73C ASN* 1.3 70.4 - - - +
75C PRO* 1.3 63.9 - - + +
76C ILE* 3.3 35.0 + - + -
77C GLU* 2.9 42.8 + - + +
78C THR* 2.6 24.5 + - - +
105C GLU* 3.2 20.3 + - - +
107C TRP* 5.1 1.2 - + - -
108C ALA* 3.7 25.8 - - + +
153C GLY 2.9 9.4 + - - +
154C GLY* 3.8 9.0 - - - +
185C CYS* 5.9 1.1 - - - -
222C TYR* 4.9 9.9 - - - -
263C PRO* 3.8 21.7 - - + +
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Residues in contact with PRO 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN 3.2 9.8 - - - +
74C HIS* 1.3 87.1 - - + +
76C ILE* 1.3 59.3 + - - +
78C THR* 3.2 8.0 + - + -
79C LEU* 2.8 39.8 + - + +
104C PHE* 3.9 12.3 - - + -
105C GLU* 3.3 28.0 - - + +
108C ALA* 3.5 22.9 - - + +
109C MET* 3.7 33.7 - - + +
110C PRO* 4.9 1.1 - - + -
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Residues in contact with ILE 76 (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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74C HIS* 3.3 19.4 + - + -
75C PRO* 1.3 80.4 - - - +
77C GLU* 1.3 64.7 + - - +
79C LEU* 4.9 0.4 - - - -
80C LEU* 3.3 55.8 + - + +
108C ALA 3.9 6.7 - - - +
110C PRO* 3.8 34.1 - - + -
113C ASP* 5.6 1.8 - - - +
116C VAL* 5.4 1.3 - - + -
263C PRO* 3.9 13.5 - - + +
266C ALA* 3.7 18.0 - - + +
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Residues in contact with GLU 77 (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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74C HIS* 2.9 26.0 + - + +
76C ILE* 1.3 76.2 - - - +
78C THR* 1.3 57.2 + - - +
81C PRO* 3.3 21.2 - - - +
150C PHE* 3.4 9.2 - - - -
152C PRO* 4.8 0.9 - - - -
153C GLY* 3.0 19.7 + - - +
184C LEU* 3.8 20.2 - - + +
185C CYS* 2.9 45.7 - - - +
262C SER 4.2 1.6 - - - -
263C PRO* 3.2 41.8 - - + +
266C ALA* 3.9 7.2 - - - -
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Residues in contact with THR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 4.2 2.9 - - + -
74C HIS 2.6 37.2 - - - +
75C PRO* 3.7 2.5 - - + -
77C GLU* 1.3 76.3 - - - +
79C LEU* 1.3 59.9 + - - +
80C LEU 3.8 0.2 - - - -
81C PRO* 4.2 2.5 - - - -
82C LEU* 3.1 30.5 - - - +
104C PHE* 3.5 28.3 - - + -
127C PHE* 3.9 17.7 - - - -
150C PHE* 3.8 6.5 - - - -
152C PRO* 3.5 29.9 - - + +
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Residues in contact with LEU 79 (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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75C PRO* 2.8 25.2 + - + +
76C ILE 4.5 0.2 - - - +
78C THR* 1.3 82.6 - - - +
80C LEU* 1.3 61.1 + - + +
81C PRO 3.5 0.2 - - - -
82C LEU* 3.4 1.9 + - + -
83C TYR* 2.8 30.6 + - - +
92C PHE* 5.7 0.2 - - + -
104C PHE* 5.0 2.2 - - + -
109C MET* 4.2 14.4 - - + -
116C VAL* 3.9 26.9 - - + +
119C PHE* 3.5 21.2 - - + -
120C PHE* 3.7 41.7 - - + -
123C HIS* 6.6 0.2 - - + -
127C PHE* 4.0 32.8 - - + -
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Residues in contact with LEU 80 (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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76C ILE* 3.3 39.2 + - + +
79C LEU* 1.3 76.7 - - - +
81C PRO* 1.3 74.2 - - + +
83C TYR* 2.9 20.7 + - + +
84C HIS* 2.9 20.2 + - + -
116C VAL* 3.8 27.1 - - + -
266C ALA* 4.2 13.2 - - + +
267C ASN* 3.8 41.5 - - + +
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Residues in contact with PRO 81 (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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76C ILE 3.8 2.2 - - - +
77C GLU 3.3 26.5 - - - +
79C LEU 3.8 1.8 - - - +
80C LEU* 1.3 96.0 - - + +
82C LEU* 1.3 56.6 + - - +
83C TYR 3.2 0.2 + - - -
84C HIS* 3.3 2.8 + - - +
85C LEU* 3.0 39.5 + - + +
150C PHE* 3.8 22.9 - - + -
182C ILE* 5.7 2.0 - - + -
266C ALA* 3.5 18.8 - - - +
269C LEU* 4.4 13.5 - - + -
270C GLY* 3.7 18.6 - - - +
273C ALA* 6.1 0.7 - - + -
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 4.3 9.9 - - + -
53C VAL* 3.8 22.4 - - + -
78C THR* 3.1 27.1 - - - +
79C LEU* 3.4 5.9 + - + +
80C LEU 3.3 0.6 - - - -
81C PRO* 1.3 79.0 - - - +
83C TYR* 1.3 57.3 + - - +
85C LEU* 4.0 10.0 - - + +
86C HIS* 3.2 27.2 + - - +
92C PHE* 3.6 53.4 - - + -
119C PHE* 3.3 8.0 - - + -
127C PHE* 3.7 21.1 - - + -
150C PHE* 3.9 13.9 - - + -
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Residues in contact with TYR 83 (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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79C LEU 2.8 18.4 + - - +
80C LEU* 2.9 12.3 + - + +
82C LEU* 1.3 76.8 - - - +
84C HIS* 1.3 71.4 + + - +
86C HIS* 3.3 5.0 + - + +
87C ALA* 3.2 23.6 + - + +
115C LYS* 4.1 32.9 + - + +
116C VAL* 5.8 9.4 - - + -
119C PHE* 3.4 41.1 - + + -
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Residues in contact with HIS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 2.9 16.4 + - + -
81C PRO 3.6 6.5 - - - +
83C TYR* 1.3 83.8 - + - +
85C LEU* 1.3 61.3 + - - +
87C ALA* 3.3 9.8 + - - +
88C ALA* 3.2 19.4 + - - +
267C ASN* 3.0 47.0 + - - -
270C GLY* 3.5 27.3 - - - +
271C LYS* 3.7 25.3 + - + +
274C ALA* 4.2 8.3 - - + +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ILE* 3.6 31.4 - - + -
81C PRO* 3.0 29.1 + - + +
82C LEU* 4.4 11.0 - - + +
84C HIS* 1.3 75.1 - - - +
86C HIS* 1.3 63.3 + - - +
88C ALA* 3.3 9.5 + - - +
90C PHE* 2.8 39.8 + - + +
150C PHE* 5.9 2.5 - - + -
182C ILE* 4.3 10.8 - - + -
270C GLY 4.9 0.4 - - - +
273C ALA* 4.1 16.2 - - + -
274C ALA* 3.9 24.9 - - + +
277C MET* 3.6 26.9 - - - -
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Residues in contact with HIS 86 (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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82C LEU 3.2 20.6 + - - +
83C TYR* 3.7 6.0 - - + +
84C HIS 3.3 0.4 - - - -
85C LEU* 1.3 73.1 - - - +
87C ALA* 1.3 68.3 + - - +
89C GLY* 3.1 14.2 + - - -
90C PHE 3.4 10.4 + - - +
91C GLU* 3.2 35.9 + - - -
92C PHE* 5.4 4.3 - + + -
119C PHE* 4.1 14.3 - + + -
122C GLN* 5.5 3.1 - - - -
123C HIS* 3.6 32.4 + + - -
91F GLU* 4.8 13.7 - - - -
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Residues in contact with ALA 87 (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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83C TYR* 3.2 14.1 + - + +
84C HIS* 3.3 13.0 - - - +
86C HIS* 1.3 76.8 + - - +
88C ALA* 1.3 55.9 + - - +
89C GLY* 3.0 10.0 + - - -
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Residues in contact with ALA 88 (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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84C HIS 3.2 10.0 + - - +
85C LEU 3.3 7.6 + - - +
86C HIS 3.2 0.8 - - - -
87C ALA* 1.3 76.5 - - - +
89C GLY* 1.3 59.6 + - - +
90C PHE* 3.3 16.0 + - + -
274C ALA* 4.2 12.6 - - + -
278C LEU* 3.9 44.2 - - + +
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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