Contacts of the helix formed by residues 56 - 70 (chain A) in PDB entry 2VF8
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 THR 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.6 4.0 - - + -
21A ALA* 4.2 13.2 - - + +
23A GLN* 4.0 9.7 - - - +
26A LEU* 4.3 4.2 - - - +
51A SER 2.5 21.4 + - - -
52A LEU* 3.3 15.3 + - + -
54A PHE 3.2 0.2 - - - -
55A GLY* 1.3 80.3 + - - +
57A LEU* 1.3 59.4 + - + +
58A TYR 3.5 0.2 - - - -
59A ALA* 4.4 0.2 - - - -
60A GLU* 2.7 38.9 + - - +
83A PRO* 4.7 2.9 - - + +
84A ASP 5.3 0.6 + - - +
85A VAL* 3.8 27.1 - - + -
88A ILE* 3.6 23.3 - - + -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.6 7.9 - - + -
18A VAL* 3.4 32.1 - - + -
33A VAL* 5.2 6.7 - - + -
41A PHE* 4.0 20.0 - - + -
52A LEU* 3.1 25.0 + - + +
53A ALA* 3.6 8.5 - - - +
56A THR* 1.3 72.6 - - + +
58A TYR* 1.3 64.4 + - - +
61A ALA* 3.0 28.7 + - - +
88A ILE* 4.0 17.9 - - + -
91A LEU* 3.8 12.3 - - + +
94A ALA* 5.5 0.9 - - - -
435A PHE* 3.6 36.1 - - + -
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA 2.9 21.6 + - - +
54A PHE* 3.6 21.8 - + + -
56A THR 3.5 0.2 - - - -
57A LEU* 1.3 73.7 - - - +
59A ALA* 1.3 56.6 + - - +
62A GLN* 2.6 77.6 + - + +
94A ALA* 3.6 40.1 + - + -
96A ALA* 3.4 40.4 + - + +
404A VAL* 4.1 12.5 - - + +
69B VAL* 4.3 11.8 + - - +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 6.1 0.2 - - - +
54A PHE 3.1 18.0 + - - +
55A GLY* 3.2 20.9 - - - +
57A LEU 3.3 0.4 - - - -
58A TYR* 1.3 82.9 - - - +
60A GLU* 1.3 66.6 + - - +
62A GLN* 3.1 19.2 - - - +
63A ARG* 3.2 9.9 + - - +
83A PRO* 3.8 12.3 - - + +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A THR* 2.7 26.1 + - - +
57A LEU 4.1 0.7 - - - +
59A ALA* 1.3 71.5 - - - +
61A ALA* 1.3 54.6 + - - +
63A ARG* 2.8 59.1 + - - +
64A ARG* 3.0 50.7 + - - +
82A VAL* 5.3 0.7 - - - +
83A PRO* 3.4 21.2 - - + +
85A VAL* 4.0 14.5 - - + +
88A ILE* 4.2 18.8 - - + -
91A LEU* 4.5 2.5 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU 3.0 18.0 + - - +
58A TYR 4.1 0.4 - - - +
60A GLU* 1.3 77.0 - - - +
62A GLN* 1.3 63.5 + - - +
63A ARG 3.2 0.3 + - - -
64A ARG* 4.5 8.3 - - - +
65A TYR* 3.5 20.8 + - - +
91A LEU* 3.5 33.4 - - + +
92A PRO 3.8 12.8 - - - +
93A PRO* 4.9 2.4 - - + +
94A ALA* 4.2 16.7 + - + +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 2.6 67.9 + - + +
59A ALA* 3.1 10.5 - - - +
61A ALA* 1.3 73.9 - - - +
63A ARG* 1.3 59.1 + - + +
65A TYR* 3.6 3.7 - - - +
66A LEU* 3.1 56.7 + - + +
94A ALA* 4.4 1.6 - - - +
658A PRO* 4.9 13.7 - - - +
65B TYR* 4.0 15.9 + - - -
69B VAL* 4.6 12.3 - - - +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA 3.5 8.1 - - - +
60A GLU* 2.8 54.1 + - - +
62A GLN* 1.3 71.6 - - + +
64A ARG* 1.3 69.3 + - - +
65A TYR 2.9 6.3 + - - -
66A LEU* 3.9 6.2 - - + +
67A GLU* 3.1 61.6 + - + +
77A PHE 6.2 0.2 - - - -
82A VAL* 3.9 38.1 - - - +
83A PRO* 4.1 3.9 - - - +
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU* 3.0 47.3 + - - +
61A ALA* 3.6 6.9 + - - +
62A GLN 3.6 0.2 - - - -
63A ARG* 1.3 85.2 - - - +
65A TYR* 1.3 61.0 + - - +
67A GLU* 4.1 9.6 + - - +
68A SER* 3.4 23.0 + - - -
87A ALA* 5.2 1.8 - - - +
88A ILE* 3.1 44.2 + - - +
91A LEU* 4.0 21.3 + - - +
396B SER* 4.5 14.7 + - - +
397B ASN* 3.6 47.4 + - + +
398B LEU* 3.9 16.0 - - + +
399B PHE* 6.1 0.4 - - - +
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Residues in contact with TYR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 3.5 15.4 + - - +
62A GLN* 3.6 3.6 - - - +
63A ARG 2.9 0.4 - - - -
64A ARG* 1.3 80.5 - - - +
66A LEU* 1.3 75.0 + - + +
68A SER* 3.0 13.4 + - - -
69A VAL* 3.0 36.4 + - + +
93A PRO* 4.3 17.0 - - + -
61B ALA 5.6 0.2 + - - -
62B GLN* 4.7 7.6 + - - +
65B TYR* 3.4 46.8 - + - +
66B LEU* 5.4 5.2 - - + -
93B PRO* 4.2 16.7 - - + +
94B ALA 3.1 30.3 + - - -
95B VAL* 4.2 8.5 - - + -
398B LEU* 4.2 21.1 - - + +
401B VAL* 5.5 1.8 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN* 3.1 49.1 + - + +
63A ARG* 3.3 7.2 + - + +
65A TYR* 1.3 88.4 - - + +
67A GLU* 1.3 58.7 + - + +
69A VAL* 4.1 8.9 - - + +
70A SER* 2.9 35.6 + - - +
74A ARG* 4.1 25.1 - - + +
658A PRO* 5.3 9.2 - - + -
65B TYR* 6.4 0.7 - - + -
66B LEU* 5.6 9.4 - - + -
69B VAL* 6.2 4.3 - - + -
656B PHE* 5.6 7.9 - - + -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG* 3.1 57.5 + - + +
64A ARG* 4.3 7.6 - - - +
65A TYR 3.2 0.2 - - - -
66A LEU* 1.3 80.3 - - + +
68A SER* 1.3 54.6 + - - +
70A SER 4.3 2.7 - - - -
71A PRO* 3.8 9.5 - - - +
74A ARG 4.4 5.1 - - - +
75A ARG* 2.7 78.8 + - - +
77A PHE 5.3 2.6 - - - +
78A ASN* 5.3 5.5 + - - -
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG 3.4 6.1 + - - -
65A TYR 3.0 7.0 + - - -
67A GLU* 1.3 77.0 - - - +
69A VAL* 1.3 66.5 + - - +
71A PRO* 3.4 2.8 - - - +
75A ARG* 4.3 4.5 + - - +
95B VAL* 4.1 17.9 - - - +
96B ALA 5.0 0.3 - - - +
389B ARG* 3.0 27.8 + - - +
393B GLN* 3.3 21.9 + - - +
396B SER* 3.7 3.1 + - - -
398B LEU* 3.1 34.3 - - - +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TYR* 3.0 54.2 + - + +
66A LEU* 4.1 8.1 - - + +
68A SER* 1.3 78.4 - - - +
70A SER* 1.3 62.6 + - - +
71A PRO* 3.1 8.7 - - - +
58B TYR* 5.6 0.9 - - - +
62B GLN* 4.1 20.2 - - - +
66B LEU* 5.6 5.8 - - + -
94B ALA 4.4 1.6 - - - +
95B VAL* 4.4 13.0 - - + -
99B GLN* 5.8 0.5 + - - -
389B ARG* 5.3 0.2 + - - -
657B LEU* 4.8 21.2 - - + +
658B PRO* 5.7 5.4 - - - +
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 2.9 22.2 + - - +
67A GLU 4.0 1.7 - - - +
69A VAL* 1.3 78.0 - - - +
71A PRO* 1.4 57.9 - - - +
72A TYR* 2.7 35.3 + - - +
73A ALA 3.4 5.5 + - - -
74A ARG* 3.5 21.5 + - - -
75A ARG 3.7 6.8 + - - -
656B PHE* 3.9 21.5 - - - -
657B LEU* 5.5 5.4 - - - -
658B PRO* 6.0 2.5 - - - -
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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