Contacts of the helix formed by residues 74 - 88 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ASN* 1.3 71.6 - - - +
75B PRO* 1.3 57.4 - - + +
76B ILE* 3.3 32.3 + - + -
77B GLU* 3.1 34.4 + - + +
78B THR* 2.5 35.3 + - - +
105B GLU* 3.5 18.6 - - - +
107B TRP* 5.6 0.7 - + - -
108B ALA* 3.8 20.6 - - + +
153B GLY 3.1 8.3 + - - -
154B GLY* 3.8 9.3 - - - -
222B TYR* 5.1 8.7 - - - -
263B PRO* 3.9 32.3 - - + +
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Residues in contact with PRO 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN 3.4 3.6 - - - +
74B HIS* 1.3 87.8 - - + +
76B ILE* 1.3 63.5 + - + +
78B THR 3.3 0.3 + - - -
79B LEU* 2.9 37.9 + - + +
104B PHE* 3.8 28.7 - - + -
105B GLU* 3.1 31.2 - - + +
108B ALA* 3.9 13.2 - - + -
109B MET* 4.1 36.6 - - + +
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B HIS* 3.3 15.7 + - + -
75B PRO* 1.3 76.4 - - + +
77B GLU* 1.3 63.5 + - - +
79B LEU* 5.0 0.7 - - - -
80B LEU* 3.1 65.0 + - + +
108B ALA 3.5 20.6 - - - +
109B MET* 4.3 14.8 - - - -
116B VAL* 4.9 14.1 - - + -
263B PRO* 4.8 6.7 - - + +
266B ALA* 3.7 6.9 - - + +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B HIS* 3.1 30.4 + - + +
76B ILE* 1.3 78.9 - - - +
78B THR* 1.3 56.3 + - - +
81B PRO* 3.1 23.7 - - - +
150B PHE* 3.6 6.9 - - - -
153B GLY* 3.0 34.4 + - - +
184B LEU* 3.7 21.2 - - + +
185B CYS* 3.0 32.8 - - - +
263B PRO* 3.1 37.8 - - + +
266B ALA* 4.0 7.6 - - - -
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASN* 4.0 4.0 - - + -
74B HIS 2.5 44.4 + - - +
75B PRO* 4.0 0.4 - - + -
76B ILE 3.2 0.2 - - - -
77B GLU* 1.3 77.3 - - + +
79B LEU* 1.3 63.7 + - - +
81B PRO* 4.0 1.1 - - - -
82B LEU* 3.1 30.2 - - - +
104B PHE* 3.4 31.7 - - + -
127B PHE* 4.1 7.9 - - - -
150B PHE* 3.7 8.3 - - - -
152B PRO* 3.4 32.3 - - + -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 2.9 21.7 + - + +
76B ILE* 4.6 0.7 - - + +
78B THR* 1.3 91.7 - - - +
80B LEU* 1.3 54.9 + - - +
81B PRO 3.4 0.4 - - - -
82B LEU* 3.2 4.7 + - + +
83B TYR* 2.7 37.6 + - - +
104B PHE* 4.5 3.1 - - + -
109B MET* 4.1 13.7 - - + -
116B VAL* 3.8 28.3 - - + +
119B PHE* 3.9 15.7 - - + -
120B PHE* 3.6 42.2 - - + +
127B PHE* 3.9 26.0 - - + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.1 35.4 + - + +
79B LEU* 1.3 77.0 - - - +
81B PRO* 1.3 69.5 - - + +
83B TYR* 3.1 9.5 + - + +
84B HIS* 3.1 28.1 + - + -
116B VAL* 4.2 31.0 - - + -
266B ALA* 3.8 14.4 - - + +
267B ASN* 3.6 42.0 - - + +
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Residues in contact with PRO 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE 3.8 0.4 - - - +
77B GLU 3.1 27.4 - - - +
78B THR 4.0 0.2 - - - -
79B LEU 3.5 2.9 - - - +
80B LEU* 1.3 95.5 - - + +
82B LEU* 1.3 62.6 + - - +
84B HIS* 2.9 6.4 + - - +
85B LEU* 2.9 32.0 + - + +
150B PHE* 3.9 21.8 - - + -
182B ILE* 5.5 3.1 - - + -
184B LEU* 5.0 0.2 - - + -
266B ALA* 3.7 17.0 - - + +
269B LEU* 4.8 11.2 - - + -
270B GLY* 3.7 19.7 - - - +
273B ALA* 5.8 1.1 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 4.1 10.5 - - + -
53B VAL* 3.8 27.1 - - + -
78B THR* 3.1 25.6 - - - +
79B LEU* 3.2 5.3 + - + +
81B PRO* 1.3 80.1 - - - +
83B TYR* 1.3 56.1 + - - +
85B LEU* 3.9 9.5 - - + +
86B HIS* 2.9 29.5 + - - +
90B PHE 4.8 0.2 - - - +
92B PHE* 3.8 41.0 - - + -
119B PHE* 3.6 7.7 - - + -
127B PHE* 3.7 27.6 - - + -
150B PHE* 3.8 15.7 - - + -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU 2.7 17.1 + - - +
80B LEU* 3.2 15.3 - - + +
82B LEU* 1.3 72.0 - - - +
84B HIS* 1.3 78.5 + + - +
86B HIS* 3.2 2.9 + - - +
87B ALA* 3.0 29.6 + - + +
115B LYS* 3.6 49.8 + - + +
116B VAL* 5.3 6.1 - - + -
119B PHE* 3.7 37.7 - + + -
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Residues in contact with HIS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 3.1 18.2 + - + -
81B PRO 2.9 7.9 + - - +
83B TYR* 1.3 89.7 - + - +
85B LEU* 1.3 62.8 + - - +
87B ALA* 3.5 6.7 + - - +
88B ALA* 3.2 22.3 + - - +
267B ASN* 2.8 36.9 + - - -
270B GLY* 3.4 23.9 + - - +
271B LYS* 3.6 32.3 + - + -
274B ALA* 4.2 6.4 - - + +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 3.7 39.3 - - + -
81B PRO* 2.9 24.1 + - + +
82B LEU* 3.9 10.3 - - + +
84B HIS* 1.3 75.6 - - - +
86B HIS* 1.3 65.8 + - - +
88B ALA* 2.9 11.0 + - - +
89B GLY 3.3 0.2 + - - -
90B PHE* 2.9 31.8 + - + +
150B PHE* 6.1 1.3 - - + -
182B ILE* 4.0 22.7 - - + -
270B GLY 4.6 0.9 - - - +
273B ALA* 3.7 13.9 - - + +
274B ALA* 3.5 33.7 - - + +
277B MET* 4.2 8.3 - - - -
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU 2.9 19.4 + - - +
83B TYR 3.2 5.8 + - - +
85B LEU* 1.3 75.2 - - - +
87B ALA* 1.3 64.9 + - - +
89B GLY* 3.2 13.7 + - - -
90B PHE 3.3 11.9 + - - +
91B GLU* 3.1 33.3 + - - +
92B PHE* 5.2 6.1 - + + -
119B PHE* 3.8 16.8 - + + -
122B GLN* 5.2 4.0 + - - -
123B HIS* 3.5 35.0 + + - -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PRO* 4.3 9.2 - - - +
83B TYR* 3.0 24.6 + - + +
84B HIS* 3.7 8.5 - - - +
86B HIS* 1.3 79.2 + - - +
88B ALA* 1.3 57.5 + - - +
89B GLY* 3.1 4.7 + - - -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PRO* 4.2 7.6 - - - -
45B TYR* 3.1 30.9 + - - +
84B HIS 3.2 15.7 + - - +
85B LEU* 2.9 8.4 + - - +
87B ALA* 1.3 74.1 - - - +
89B GLY* 1.3 58.2 + - - +
90B PHE* 3.3 9.2 + - + -
274B ALA* 4.3 10.5 - - + -
278B LEU* 3.8 30.2 - - + +
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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