Contacts of the helix formed by residues 69 - 85 (chain B) in PDB entry 3FVS
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 TYR 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.6 34.1 - - + +
64B THR* 3.4 24.6 - - + +
68B GLY* 1.3 69.7 - - - -
70B PRO* 1.4 73.7 - - + +
71B PRO* 3.5 39.8 - - + +
72B LEU* 2.9 24.3 + - + +
73B THR 3.1 10.4 + - - -
282B THR* 4.3 6.5 - - + -
285B GLN* 2.8 37.2 + - + +
286B ALA* 3.5 38.0 - - + +
289B ALA* 4.8 0.9 - - + -
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Residues in contact with PRO 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 3.8 12.1 - - - +
65B LYS* 3.8 23.3 - - + -
68B GLY 3.4 6.3 - - - +
69B TYR* 1.4 83.3 - - + +
71B PRO* 1.4 71.2 - - + +
73B THR* 3.2 10.4 + - - +
74B LYS* 2.9 27.6 + - - +
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Residues in contact with PRO 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 3.5 41.7 - - + +
70B PRO* 1.4 94.1 - - + +
72B LEU* 1.3 59.1 + - - +
74B LYS* 3.7 10.2 - - + +
75B ILE* 3.2 24.8 + - - +
289B ALA* 3.9 9.4 - - + +
293B GLU* 4.5 10.7 - - - +
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Residues in contact with LEU 72 (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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69B TYR* 2.9 16.7 + - + +
71B PRO* 1.3 77.2 - - - +
73B THR* 1.3 64.9 - - - +
75B ILE* 3.3 5.3 + - + +
76B LEU* 2.9 52.2 + - + +
96B VAL* 3.8 25.8 - - + -
256B VAL* 4.2 10.1 - - + -
258B TRP* 5.7 1.1 - - + -
285B GLN* 3.8 40.2 - - + +
288B VAL* 3.7 24.2 - - + +
289B ALA* 3.6 17.8 - - - +
292B PHE* 4.6 0.7 - - + -
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Residues in contact with THR 73 (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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67B PHE 3.9 7.0 - - - +
68B GLY* 3.8 30.4 + - - +
69B TYR 3.1 2.7 + - - +
70B PRO* 3.2 16.8 + - - +
72B LEU* 1.3 75.5 - - - +
74B LYS* 1.3 64.3 + - - +
76B LEU* 3.9 1.0 - - - +
77B ALA* 3.0 27.2 + - - +
90B PRO* 3.5 30.2 + - - +
94B VAL* 3.9 19.0 - - + +
96B VAL* 3.9 13.5 - - + -
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Residues in contact with LYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PRO 2.9 18.6 + - - +
71B PRO* 3.7 9.6 - - + +
72B LEU 3.1 0.2 - - - -
73B THR* 1.3 79.0 + - - +
75B ILE* 1.3 58.9 + - + +
77B ALA* 3.4 2.3 + - - +
78B SER* 3.0 28.6 + - - -
90B PRO* 4.3 13.9 - - + -
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Residues in contact with ILE 75 (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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71B PRO 3.2 12.0 + - - +
72B LEU* 3.4 13.0 - - + +
74B LYS* 1.3 77.0 - - - +
76B LEU* 1.3 68.5 + - - +
78B SER* 4.4 4.5 - - - -
79B PHE* 2.8 32.3 + - + +
289B ALA* 3.9 26.5 - - + +
292B PHE* 3.9 26.0 - - + +
293B GLU* 4.0 27.6 - - + +
296B GLN* 3.1 37.7 - - + +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 2.9 40.9 + - + +
73B THR 3.9 3.1 - - - +
75B ILE* 1.3 77.2 - - - +
77B ALA* 1.3 58.0 + - - +
79B PHE* 4.9 0.2 - - - -
80B PHE* 2.9 63.9 + - + +
88B ILE* 4.8 0.3 - - - +
94B VAL* 3.8 21.8 - - + -
96B VAL* 4.5 4.7 - - + -
258B TRP* 3.8 39.7 - - + -
260B LEU* 4.7 4.9 - - + +
292B PHE* 3.7 25.6 - - + -
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Residues in contact with ALA 77 (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 THR 3.0 19.2 + - - +
74B LYS 3.8 3.6 - - - +
76B LEU* 1.3 75.6 - - - +
78B SER* 1.3 58.6 + - - +
81B GLY* 3.0 27.4 + - - -
88B ILE* 3.4 47.2 + - + +
90B PRO* 4.0 17.0 - - + -
94B VAL* 4.2 1.5 - - + +
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Residues in contact with SER 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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74B LYS* 3.0 19.9 + - - -
75B ILE* 3.9 9.0 - - - -
77B ALA* 1.3 77.2 - - - +
79B PHE* 1.3 62.3 + - - +
81B GLY* 3.8 0.5 - - - -
82B GLU* 3.2 22.3 + - - +
296B GLN* 3.0 20.1 + - - -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 2.8 27.1 + - + +
76B LEU* 4.4 0.4 - - - +
78B SER* 1.3 70.4 - - - +
80B PHE* 1.3 70.7 + + + +
82B GLU* 3.3 30.6 + - - +
83B LEU* 3.1 27.6 + - + +
218B TRP* 3.7 37.7 - + - -
292B PHE* 3.8 32.5 - + + -
295B GLU 5.0 0.4 - - - -
296B GLN* 3.7 46.4 - - + +
299B PHE* 3.9 22.4 - + - -
306B PHE* 4.0 9.4 - + - -
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 2.9 49.7 + - + +
79B PHE* 1.3 83.2 - + - +
81B GLY* 1.3 59.3 + - - +
83B LEU* 3.6 23.1 - - + -
84B LEU* 2.8 39.3 + - + +
88B ILE* 3.9 4.5 - - + -
217B GLN* 3.5 27.4 - - - -
218B TRP* 4.5 5.6 - + - -
241B THR* 6.3 1.8 - - + -
248B THR* 6.0 0.2 - - - -
258B TRP* 3.9 22.0 - + - -
260B LEU* 3.6 31.0 - - + -
292B PHE* 3.8 24.0 - + - -
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Residues in contact with GLY 81 (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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77B ALA 3.0 23.5 + - - -
78B SER 3.8 0.4 - - - -
80B PHE* 1.3 76.7 - - - +
82B GLU* 1.3 56.1 + - - +
85B GLY* 2.9 10.7 + - - -
86B GLN* 2.9 45.1 + - - -
88B ILE* 3.6 8.8 - - - +
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Residues in contact with GLU 82 (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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78B SER 3.2 13.4 + - - +
79B PHE* 3.4 31.3 - - - +
81B GLY* 1.3 76.3 - - - +
83B LEU* 1.3 78.1 + - - +
84B LEU 3.5 0.3 + - - -
85B GLY* 3.5 8.2 + - - -
296B GLN* 5.6 6.0 - - - +
299B PHE* 3.5 28.1 - - - +
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Residues in contact with LEU 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 PHE* 3.1 22.6 + - + +
80B PHE* 3.2 33.4 + - + +
82B GLU* 1.3 86.1 - - - +
84B LEU* 1.3 65.1 + - + +
85B GLY 3.7 0.2 + - - -
217B GLN* 3.9 10.3 - - - +
218B TRP* 3.7 28.0 - - + -
228B SER* 6.0 0.3 - - - -
231B SER* 5.0 3.3 - - - -
299B PHE* 3.4 34.5 - - + -
300B ARG* 5.7 1.8 - - - +
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Residues in contact with LEU 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 PHE* 2.8 24.1 + - + +
83B LEU* 1.3 80.7 - - + +
85B GLY* 1.3 63.8 + - - +
86B GLN* 4.0 13.4 - - + +
88B ILE* 4.2 9.2 - - + -
228B SER* 3.2 37.7 - - - +
230B ALA* 4.2 16.3 - - + +
231B SER* 3.4 32.5 - - - +
236B TRP* 3.9 27.4 - - + -
241B THR* 4.9 8.7 - - + +
260B LEU* 4.2 15.7 - - + -
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Residues in contact with GLY 85 (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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81B GLY 2.9 6.9 + - - -
82B GLU 3.5 6.0 + - - -
83B LEU 3.4 4.0 + - - -
84B LEU* 1.3 79.5 - - - +
86B GLN* 1.3 60.9 + - - +
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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