Contacts of the helix formed by residues 53 - 65 (chain C) in PDB entry 2FRV
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C ALA* 1.3 71.9 - - - +
54C HIS* 1.3 62.2 + - - -
56C VAL* 3.0 22.1 + - - +
57C GLU* 3.5 3.6 + - - +
10D VAL 5.2 1.8 - - - -
11D VAL* 3.7 7.4 - - - +
12D ASP 3.7 28.9 - - - -
13D PRO* 2.8 22.3 + - - +
174D TYR* 4.8 0.7 - - - -
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Residues in contact with HIS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ALA 3.5 0.4 + - - -
53C GLY* 1.3 70.5 - - - -
55C ALA* 1.3 61.7 + - - +
56C VAL 3.2 0.2 - - - -
57C GLU* 3.8 12.3 - - + +
58C GLU* 3.1 41.0 + - - +
10D VAL* 4.4 22.7 + - + +
12D ASP 4.4 7.8 + - - -
194I PHE* 4.5 20.2 - + - -
195I GLU* 3.7 44.2 + - + +
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C GLY* 4.6 1.3 - - - -
52C ALA 3.3 16.0 + - - +
53C GLY 3.2 2.0 + - - -
54C HIS* 1.3 76.0 - - - +
56C VAL* 1.3 60.2 + - - +
58C GLU* 3.7 4.9 + - - -
59C ALA* 3.4 5.7 + - - +
171D THR 4.8 0.2 - - - +
172D ASN* 2.5 63.1 + - + +
174D TYR* 4.4 11.0 - - + -
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 3.5 18.0 - - + -
49C MET* 3.8 24.2 - - + -
51C GLY* 3.2 33.2 - - - +
53C GLY 3.0 26.4 + - - +
55C ALA* 1.3 76.7 - - - +
57C GLU* 1.3 71.6 + - - +
58C GLU 3.3 0.4 - - - -
59C ALA* 3.1 8.2 - - - +
60C LEU 2.9 23.7 + - - -
13D PRO* 3.7 17.9 - - + -
15D THR* 3.9 9.4 - - + -
171D THR 5.1 3.8 - - - +
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 2.8 30.5 + - - -
53C GLY 3.5 5.3 + - - +
54C HIS* 3.3 15.7 + - + +
56C VAL* 1.3 75.8 - - - +
58C GLU* 1.3 58.8 + - + +
60C LEU* 4.0 16.9 - - - +
61C HIS* 3.0 28.1 + - - +
87C VAL* 4.3 11.3 - - - +
88C GLY* 5.8 3.8 - - - -
90C ARG* 6.0 2.9 + - - -
95C ILE* 5.7 4.5 - - - +
12D ASP 4.4 4.9 - - - +
13D PRO* 3.4 28.8 - - + +
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C HIS* 3.1 35.1 + - - +
55C ALA* 3.8 8.8 - - - +
57C GLU* 1.3 76.4 - - - +
59C ALA* 1.3 56.8 + - - +
61C HIS* 3.4 6.7 + - - +
62C GLU* 3.1 35.9 + - + +
172D ASN* 4.0 9.0 + - - +
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ASP 4.5 15.2 - - - +
44C TYR* 4.8 0.4 - - + -
49C MET* 4.6 5.6 - - + -
55C ALA 3.4 11.3 + - - +
56C VAL* 3.1 14.3 + - - +
58C GLU* 1.3 76.6 - - - +
60C LEU* 1.3 67.4 + - - +
61C HIS 3.2 0.2 - - - -
62C GLU* 4.2 4.2 - - - +
63C ALA* 2.9 27.0 + - - +
171D THR* 4.2 20.9 - - + +
172D ASN* 3.8 8.7 - - - +
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 3.2 35.9 - - + -
12C LEU* 4.2 13.0 - - + -
44C TYR* 3.6 44.6 - - + +
56C VAL 2.9 12.0 + - - +
57C GLU* 4.1 20.0 - - - +
59C ALA* 1.3 80.3 - - - +
61C HIS* 1.3 64.7 + - - +
63C ALA* 3.0 9.6 + - - +
64C ILE* 3.1 29.7 + - + +
90C ARG* 6.1 1.3 - - - +
95C ILE* 4.3 15.7 - - + -
98C GLU* 6.5 0.4 - - - -
99C VAL* 4.4 7.0 - - + -
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Residues in contact with HIS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU 3.0 18.9 + - - +
58C GLU* 3.5 8.1 - - - +
59C ALA 3.2 0.2 - - - -
60C LEU* 1.3 79.0 - - - +
62C GLU* 1.3 82.8 + - - +
64C ILE* 3.6 17.5 - - - +
65C LYS* 3.5 20.5 - - - +
98C GLU* 4.8 3.6 + - - -
215I TYR* 3.9 23.3 + + - -
222I PRO* 4.3 21.0 + - + +
223I ASP* 2.7 39.5 + - - -
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Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLU* 3.1 19.0 + - + +
59C ALA* 4.2 4.5 - - - +
60C LEU 3.3 0.2 - - - -
61C HIS* 1.3 86.2 - - - +
63C ALA* 1.3 67.7 + - - +
64C ILE 3.2 0.4 - - - -
65C LYS* 2.9 52.7 + - - +
66C GLY 4.2 1.4 + - - -
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C SER* 4.7 3.6 + - - +
10C VAL* 3.7 23.6 - - + -
43C ASP* 4.0 23.1 - - + +
59C ALA 2.9 19.4 + - - +
60C LEU* 3.6 3.6 - - - +
62C GLU* 1.3 79.5 - - - +
64C ILE* 1.3 58.2 + - - +
65C LYS 3.1 4.0 + - - -
66C GLY* 3.2 12.8 + - - -
68C PHE* 3.8 13.7 - - - +
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 4.2 6.3 - - + -
60C LEU* 3.1 34.4 + - + +
61C HIS* 3.6 22.7 - - - +
63C ALA* 1.3 74.6 - - - +
65C LYS* 1.3 62.9 + - + +
66C GLY 3.2 2.9 + - - +
68C PHE* 3.5 36.6 - - + -
98C GLU* 3.7 28.5 - - + +
99C VAL* 3.9 24.9 - - + -
102C LYS* 3.9 28.9 - - + +
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C HIS* 3.5 27.3 + - - +
62C GLU* 2.9 42.9 + - - +
63C ALA 3.1 1.0 - - - -
64C ILE* 1.3 79.8 - - + +
66C GLY* 1.3 55.4 + - - +
222I PRO 5.6 0.4 + - - -
223I ASP* 2.8 32.7 + - - +
258I TYR* 5.2 4.4 + - - -
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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