Contacts of the helix formed by residues 53 - 65 (chain A) in PDB entry 2FV7
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 GLY 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A SER* 3.8 9.4 - - - -
25A MET* 3.4 26.5 - - - +
52A GLY* 1.3 73.3 - - - +
54A LYS* 1.3 60.3 + - - -
55A GLY 3.3 2.7 - - - -
56A ALA 3.5 0.3 + - - -
57A ASN* 2.9 35.6 + - - +
154A GLU* 3.7 10.1 - - - -
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Residues in contact with LYS 54 (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 SER* 4.3 0.7 - - - +
53A GLY* 1.3 72.1 - - - -
55A GLY* 1.3 56.5 + - - +
57A ASN* 3.3 1.2 + - - +
58A GLN* 2.9 37.0 + - - +
152A GLN* 4.0 13.2 - - + -
154A GLU* 2.9 34.3 + - - +
177A ASN* 4.5 2.0 - - - +
179A ALA* 3.5 50.2 - - + +
180A PRO* 4.0 7.0 - - - -
202A GLU* 4.5 3.6 + - - -
269A ASP* 3.6 16.6 - - - +
404A MG 4.0 10.5 - - - -
510A UNX 2.5 36.6 - - - -
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Residues in contact with GLY 55 (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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20A VAL* 3.4 11.4 - - - +
23A SER* 3.4 14.7 + - - -
53A GLY 3.3 0.4 - - - -
54A LYS* 1.3 79.3 - - - +
56A ALA* 1.3 56.2 + - - +
58A GLN* 3.3 0.7 + - - +
59A CYS* 2.9 29.3 + - - +
71A MET* 3.7 10.1 - - - -
152A GLN* 3.4 27.3 + - - -
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Residues in contact with ALA 56 (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 SER 3.0 16.1 + - - +
24A CYS* 4.0 6.5 - - - -
52A GLY 3.8 2.5 - - - +
54A LYS 3.4 0.2 - - - -
55A GLY* 1.3 73.2 - - - +
57A ASN* 1.3 53.5 + - - +
59A CYS* 3.1 1.7 + - - +
60A VAL* 2.7 38.3 + - - +
71A MET* 3.6 11.9 - - - +
84A TYR* 3.0 42.6 - - + +
88A LEU* 4.5 7.2 - - + -
308A GLN* 3.8 4.0 - - - +
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Residues in contact with ASN 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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52A GLY* 3.8 9.0 - - - -
53A GLY 2.9 30.6 + - - +
54A LYS 3.4 2.0 - - - +
56A ALA* 1.3 75.8 - - - +
58A GLN* 1.3 63.2 + - - +
60A VAL* 3.3 0.9 + - - +
61A GLN* 3.1 18.2 + - - +
266A GLY* 4.8 1.0 - - - -
269A ASP* 2.8 35.1 + - + -
307A THR* 3.7 20.0 - - - +
308A GLN* 3.0 29.5 + - - +
311A TYR* 3.3 25.7 + - - +
510A UNX 4.3 3.0 - - - -
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Residues in contact with GLN 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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20A VAL* 4.9 3.8 - - + -
54A LYS 2.9 20.8 + - - +
55A GLY 3.6 3.4 - - - +
57A ASN* 1.3 73.1 - - - +
59A CYS* 1.3 62.8 + - - +
61A GLN 3.2 2.4 + - - -
62A ALA* 3.0 20.7 + - - +
150A VAL* 3.2 18.1 - - + +
152A GLN* 2.8 33.9 + - - +
177A ASN* 3.0 30.4 + - - +
269A ASP* 3.0 40.9 + - - +
272A VAL* 3.5 18.2 - - + +
273A GLY* 3.3 16.6 - - - +
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Residues in contact with CYS 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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20A VAL* 3.7 23.5 - - + +
55A GLY 2.9 17.1 + - - +
56A ALA* 3.1 4.0 + - - +
58A GLN* 1.3 75.2 - - - +
60A VAL* 1.3 59.9 + - - +
62A ALA* 3.5 4.7 + - - +
63A ALA* 2.9 31.0 + - - +
69A THR* 3.5 28.2 - - - +
70A SER 4.2 5.6 - - - -
71A MET* 3.7 15.7 - - - -
93A ILE* 3.6 23.1 - - + -
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Residues in contact with VAL 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 ALA 2.7 22.8 + - - +
57A ASN 3.7 3.1 - - - +
59A CYS* 1.3 73.1 - - - +
61A GLN* 1.3 63.0 + - - +
63A ALA* 3.2 2.6 + - - +
64A ARG* 2.9 56.9 + - - +
87A ASN* 4.9 0.9 - - - +
88A LEU* 4.9 4.7 - - + -
91A ASN* 3.7 17.7 - - - +
93A ILE* 3.7 21.3 - - + -
308A GLN* 3.7 27.6 - - + +
311A TYR* 3.9 14.4 - - + -
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Residues in contact with GLN 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 ASN 3.1 9.4 + - - +
58A GLN 3.7 6.7 - - - +
60A VAL* 1.3 78.1 - - - +
62A ALA* 1.3 63.5 + - - +
64A ARG* 3.3 1.0 + - - +
65A LEU* 3.2 30.3 + - + +
270A SER* 2.5 50.2 + - - +
273A GLY* 4.3 1.3 - - - -
274A ALA 4.0 7.0 - - - +
297A ILE* 3.7 12.4 - - + +
311A TYR* 3.3 33.0 - - + +
312A PRO* 3.0 35.7 + - - +
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Residues in contact with ALA 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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18A VAL* 4.4 14.8 - - + -
58A GLN 3.0 14.3 + - - +
59A CYS* 3.9 5.2 - - - +
61A GLN* 1.3 75.1 - - - +
63A ALA* 1.3 62.9 + - - +
65A LEU* 3.3 10.8 + - - +
66A GLY 3.5 0.5 + - - -
67A ALA* 3.1 30.0 + - + +
69A THR* 4.1 12.6 - - + -
273A GLY* 3.3 24.1 + - - +
276A ALA* 4.9 0.2 - - + -
277A PHE* 4.5 8.1 - - + +
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Residues in contact with ALA 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 CYS 2.9 18.4 + - - +
60A VAL* 3.5 5.2 - - - +
62A ALA* 1.3 75.5 - - - +
64A ARG* 1.3 57.5 + - + +
66A GLY* 2.9 21.8 + - - -
67A ALA 3.7 14.9 + - - +
69A THR* 3.8 7.7 - - - +
91A ASN* 3.3 25.4 - - + +
92A ASP* 4.8 3.9 - - + +
93A ILE* 3.7 15.3 - - + -
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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 VAL* 2.9 34.7 + - + +
61A GLN* 3.3 4.7 + - - +
63A ALA* 1.3 72.7 - - + +
65A LEU* 1.3 58.2 + - - +
66A GLY* 3.1 1.5 + - - -
91A ASN* 3.1 33.1 + - - +
308A GLN* 2.8 34.3 + - - +
309A SER* 4.0 9.3 + - - +
311A TYR* 2.8 38.4 + - - +
312A PRO 3.5 13.9 - - - +
313A TYR* 3.6 50.1 + - + -
314A LYS* 3.0 23.5 + - - +
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Residues in contact with LEU 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 GLN* 3.2 28.8 + - - +
62A ALA 3.6 8.1 - - - +
63A ALA 3.2 0.4 - - - -
64A ARG* 1.3 76.2 - - - +
66A GLY* 1.3 56.8 + - - +
67A ALA 3.6 0.9 - - - -
274A ALA* 3.6 37.7 - - + +
277A PHE* 3.2 44.0 - - + -
278A TYR* 4.9 2.2 - - + -
297A ILE* 4.0 11.2 - - + -
312A PRO 4.3 2.9 - - - +
314A LYS* 3.6 23.3 - - - +
317A LEU* 3.4 32.8 - - + -
322A PHE* 4.3 8.9 - - + -
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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