Contacts of the helix formed by residues 53 - 66 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B SER* 3.8 10.1 - - - -
25B MET* 3.9 21.4 - - - +
27B ASP* 4.7 0.8 + - - -
52B GLY* 1.3 72.2 - - - -
54B LYS* 1.3 60.7 + - - -
55B GLY 3.3 2.9 - - - -
56B ALA 3.3 1.6 + - - -
57B ASN* 2.8 34.0 + - - +
154B GLU* 3.8 9.2 - - - -
503B UNX 3.6 10.0 - - - -
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Residues in contact with LYS 54 (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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23B SER* 4.2 0.2 - - - +
53B GLY* 1.3 68.5 - - - -
55B GLY* 1.3 65.8 + - - +
57B ASN* 3.6 0.5 - - - +
58B GLN* 3.0 32.0 + - - +
152B GLN* 4.0 13.7 - - + -
154B GLU* 3.1 33.2 + - - +
177B ASN* 4.3 3.6 - - - +
179B ALA* 3.5 48.9 - - + +
180B PRO* 3.8 6.5 - - - +
202B GLU* 4.6 4.2 + - - -
269B ASP* 3.6 27.1 + - - +
406B MG 4.3 12.5 - - - -
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Residues in contact with GLY 55 (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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20B VAL* 3.5 15.5 - - - +
23B SER* 3.3 17.4 + - - -
53B GLY 3.3 0.6 - - - -
54B LYS* 1.3 79.8 - - - +
56B ALA* 1.3 56.1 + - - +
58B GLN* 3.3 0.7 + - - +
59B CYS* 3.0 24.4 + - - +
71B MET* 3.7 7.0 - - - -
152B GLN* 3.4 26.7 + - - -
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Residues in contact with ALA 56 (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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23B SER 3.0 16.5 + - - +
24B CYS* 4.0 6.7 - - - -
52B GLY 3.8 2.2 - - - +
53B GLY 3.3 0.2 + - - -
55B GLY* 1.3 73.5 - - - +
57B ASN* 1.3 57.6 + - - +
59B CYS* 3.2 3.0 + - - +
60B VAL* 2.8 33.8 + - - +
71B MET* 3.7 10.4 - - - +
84B TYR* 2.8 44.9 - - + +
88B LEU* 4.4 6.5 - - + -
308B GLN* 3.8 3.8 - - - +
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Residues in contact with ASN 57 (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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51B PHE 3.9 0.2 - - - +
52B GLY* 3.5 7.6 - - - -
53B GLY 2.8 21.7 + - - +
54B LYS 3.6 0.7 - - - +
56B ALA* 1.3 76.7 - - - +
58B GLN* 1.3 61.8 + - - +
60B VAL 3.4 0.3 + - - -
61B GLN* 3.1 19.9 + - - +
266B GLY* 4.8 0.6 - - - -
269B ASP* 2.7 37.4 + - + +
307B THR* 3.5 13.2 - - - +
308B GLN* 2.8 30.2 + - - +
311B TYR* 3.2 23.6 + - - +
503B UNX 3.0 24.4 - - - -
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Residues in contact with GLN 58 (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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20B VAL* 4.8 4.0 - - + -
54B LYS* 3.0 18.4 + - - +
55B GLY 3.6 3.8 - - - +
57B ASN* 1.3 73.2 - - - +
59B CYS* 1.3 65.1 + - - +
61B GLN 3.4 0.7 + - - -
62B ALA* 3.2 20.4 + - - +
150B VAL* 3.1 19.5 - - + +
152B GLN* 2.8 30.7 + - - +
177B ASN* 3.1 24.9 + - - +
269B ASP* 3.1 46.9 + - - +
272B VAL* 3.3 19.6 - - + +
273B GLY* 3.3 16.0 - - - +
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Residues in contact with CYS 59 (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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20B VAL* 3.8 22.8 - - + +
55B GLY 3.0 16.6 + - - +
56B ALA* 3.5 4.9 - - - +
58B GLN* 1.3 76.2 - - - +
60B VAL* 1.3 58.0 + - - +
62B ALA* 3.4 5.8 + - - +
63B ALA* 2.9 30.1 + - - +
69B THR* 3.6 20.7 - - - +
70B SER 4.4 0.4 - - - -
71B MET* 3.8 22.0 - - - -
93B ILE* 3.6 35.9 - - + -
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Residues in contact with VAL 60 (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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56B ALA 2.8 20.8 + - - +
57B ASN 3.7 4.7 - - - +
59B CYS* 1.3 75.9 - - - +
61B GLN* 1.3 63.6 + - - +
63B ALA* 3.4 2.6 + - - +
64B ARG* 3.1 54.5 + - - +
87B ASN* 4.9 2.9 - - - +
88B LEU* 5.0 2.9 - - + -
91B ASN* 3.8 14.8 - - - +
93B ILE* 3.7 21.3 - - + -
308B GLN* 3.6 28.3 - - + +
311B TYR* 3.9 13.7 - - + -
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Residues in contact with GLN 61 (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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57B ASN 3.1 16.5 + - - +
58B GLN 3.4 4.0 + - - +
59B CYS 3.4 0.2 - - - -
60B VAL* 1.3 77.0 - - - +
62B ALA* 1.3 61.7 + - - +
64B ARG* 3.5 1.0 + - - +
65B LEU* 3.2 29.1 + - + +
270B SER* 2.7 49.0 + - - +
273B GLY* 4.2 2.9 - - - -
274B ALA 3.9 7.4 - - - +
297B ILE* 3.5 12.8 - - + +
311B TYR* 3.3 28.8 - - + +
312B PRO* 3.1 34.7 + - - +
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Residues in contact with ALA 62 (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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18B VAL* 4.7 10.8 - - + -
20B VAL* 6.1 0.2 - - + -
58B GLN 3.2 13.1 + - - +
59B CYS* 3.8 4.7 - - - +
61B GLN* 1.3 77.8 - - - +
63B ALA* 1.3 61.6 + - - +
65B LEU* 3.4 9.5 + - - +
66B GLY 3.4 0.5 + - - -
67B ALA* 2.9 33.6 + - + +
69B THR* 4.0 13.0 - - + -
273B GLY* 3.4 22.6 + - - +
276B ALA* 4.7 0.4 - - + -
277B PHE* 4.3 10.9 - - + +
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Residues in contact with ALA 63 (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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59B CYS 2.9 17.5 + - - +
60B VAL* 3.7 5.6 - - - +
61B GLN 3.3 0.2 - - - -
62B ALA* 1.3 76.5 - - - +
64B ARG* 1.3 58.2 + - + +
66B GLY* 3.1 18.7 + - - -
67B ALA 3.6 14.5 + - - +
69B THR* 3.8 8.6 - - - +
91B ASN* 3.5 25.8 - - + +
92B ASP* 4.8 4.1 - - + +
93B ILE* 3.8 15.5 - - + -
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Residues in contact with ARG 64 (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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60B VAL* 3.1 27.9 + - - +
61B GLN* 4.0 3.4 - - - +
62B ALA 3.4 0.2 - - - -
63B ALA* 1.3 71.7 - - + +
65B LEU* 1.3 61.7 + - - +
66B GLY* 3.2 3.0 + - - -
87B ASN* 5.7 0.2 + - - -
91B ASN* 2.9 37.1 + - + +
308B GLN* 2.7 34.0 + - - +
309B SER* 4.5 6.9 + - - +
311B TYR* 2.9 29.4 + - - +
312B PRO 3.6 12.8 - - - +
313B TYR* 3.3 49.7 + - + -
314B LYS* 2.9 24.8 + - - +
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Residues in contact with LEU 65 (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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61B GLN* 3.2 28.3 + - - +
62B ALA 3.7 5.6 - - - +
63B ALA 3.3 0.6 - - - -
64B ARG* 1.3 76.9 - - - +
66B GLY* 1.3 57.7 + - - +
67B ALA 3.8 0.4 - - - -
274B ALA* 3.6 36.8 - - + +
277B PHE* 3.6 40.8 - - + -
278B TYR* 5.1 1.6 - - + +
297B ILE* 3.3 30.5 - - + -
312B PRO 4.6 1.8 - - - +
314B LYS* 3.4 26.5 - - - +
317B LEU* 3.5 15.0 - - + -
322B PHE* 4.0 13.7 - - + -
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Residues in contact with GLY 66 (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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63B ALA 3.1 10.0 + - - -
64B ARG 3.2 1.6 - - - -
65B LEU* 1.3 80.2 - - - +
67B ALA* 1.3 64.9 + - - +
68B MET* 3.7 4.9 + - - +
277B PHE* 4.4 5.8 - - - -
281B TYR* 4.4 5.6 + - - -
314B LYS* 4.7 7.6 - - - -
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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