Contacts of the helix formed by residues 48 - 61 (chain B) in PDB entry 2FA5
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 ALA 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B TYR* 3.9 3.5 - - - -
46B GLY 4.3 0.2 + - - -
47B MSE 1.3 77.5 - - - +
49B ILE* 1.3 67.1 + - - +
50B PRO* 3.3 15.3 - - + -
51B GLU* 3.0 29.0 + - - +
52B TRP 3.1 18.2 + - - -
86B ARG* 5.4 3.1 - - - +
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Residues in contact with ILE 49 (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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31B ASN 5.5 1.1 - - - +
34B SER* 4.1 39.0 - - - +
35B GLY* 4.4 5.4 - - - +
38B ALA* 4.0 15.5 - - + +
41B TYR* 3.3 18.4 - - - +
48B ALA* 1.3 71.7 - - - +
50B PRO* 1.3 73.2 - - + +
52B TRP* 3.3 6.3 + - + +
53B ARG* 3.1 21.2 + - + +
75B MSE 5.8 3.8 - - + -
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Residues in contact with PRO 50 (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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48B ALA* 3.5 13.7 - - + -
49B ILE* 1.3 96.2 - - + +
51B GLU* 1.3 63.2 + - + +
53B ARG* 3.3 3.9 + - + +
54B VAL* 3.1 27.4 + - - +
75B MSE 3.7 30.0 - - + +
79B ALA* 4.6 14.1 - - + +
80B VAL* 5.8 0.4 - - - -
83B ALA* 3.9 16.6 - - + -
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Residues in contact with GLU 51 (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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46B GLY 4.3 3.6 - - - +
47B MSE 3.6 18.2 - - + +
48B ALA* 3.0 38.2 + - + +
50B PRO* 1.3 75.4 - - - +
52B TRP* 1.3 66.5 + - - +
54B VAL 3.3 1.7 + - - -
55B ILE* 3.1 20.3 + - - +
83B ALA* 3.8 30.7 - - + +
86B ARG* 2.5 45.1 + - - -
87B LEU* 3.5 24.8 - - + +
90B ARG* 5.5 1.2 + - - -
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Residues in contact with TRP 52 (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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16A LEU* 4.2 8.1 - - + -
37B ILE* 4.5 1.8 - - + +
41B TYR* 3.4 46.7 - + + +
47B MSE 4.0 19.0 - - - +
48B ALA 3.1 5.9 + - - -
49B ILE* 3.7 3.1 - - + +
51B GLU* 1.3 75.8 - - - +
53B ARG* 1.3 69.2 + - - +
55B ILE* 3.1 16.3 + - + +
56B THR* 3.0 38.7 + - + +
116B VAL* 4.6 2.2 - - + -
117B TYR* 4.0 29.2 - + - -
120B VAL* 3.5 42.6 - - + -
121B ALA* 3.8 11.4 - - - -
124B VAL* 4.0 13.7 - - + +
801B CL 3.2 29.7 - - + +
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Residues in contact with ARG 53 (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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18A LEU* 4.0 5.7 - - - +
23A PRO* 5.3 4.0 + - - +
24A TYR* 3.7 46.5 - - - +
27A SER* 5.4 8.1 + - - -
34B SER* 5.4 5.7 + - - -
37B ILE* 6.0 0.4 - - - +
49B ILE* 3.1 15.1 + - + +
50B PRO* 3.5 12.8 - - + +
51B GLU 3.2 0.2 - - - -
52B TRP* 1.3 80.5 - - - +
54B VAL* 1.3 63.8 + - + +
56B THR* 2.7 45.0 + - - +
57B ILE* 3.0 19.5 + - + +
69B VAL* 5.6 1.3 - - + -
73B THR* 4.2 9.0 - - + -
75B MSE 3.9 24.9 - - + -
801B CL 3.3 31.9 - - - +
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Residues in contact with VAL 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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50B PRO 3.1 15.2 + - - +
51B GLU 3.3 7.4 + - - +
53B ARG* 1.3 76.5 - - + +
55B ILE* 1.3 64.3 + - - +
57B ILE* 3.2 7.1 + - - +
58B LEU* 2.9 45.6 + - + +
69B VAL* 4.3 22.2 - - + -
75B MSE 6.2 1.3 - - - -
80B VAL* 4.7 5.8 - - + -
83B ALA* 4.1 17.7 - - + -
84B VAL* 4.4 22.4 - - + -
87B LEU* 3.7 16.8 - - + -
93B ILE* 4.6 1.6 - - + -
107B LEU* 5.5 0.4 - - + -
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Residues in contact with ILE 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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47B MSE 3.5 39.3 - - + -
51B GLU 3.1 9.2 + - - +
52B TRP* 3.1 18.2 + - + +
54B VAL* 1.3 78.9 - - - +
56B THR* 1.3 63.5 + - - +
58B LEU 3.3 0.2 + - - -
59B ALA* 3.1 21.7 + - - +
87B LEU* 4.0 17.7 - - + -
92B PHE* 4.5 9.6 - - + -
93B ILE* 4.7 2.9 - - + -
109B LEU* 3.7 26.9 - - + +
113B GLY 4.5 6.1 - - - +
116B VAL* 4.7 7.0 - - + -
117B TYR* 3.9 29.8 - - + -
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Residues in contact with THR 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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16A LEU* 3.6 16.2 - - + +
18A LEU* 3.6 25.7 - - - +
52B TRP* 3.0 57.4 + - + +
53B ARG* 2.7 37.1 + - - +
55B ILE* 1.3 74.4 - - - +
57B ILE* 1.3 61.1 + - - +
59B ALA* 3.4 3.6 + - - +
60B LEU* 3.4 17.3 + - - +
117B TYR* 4.2 13.4 + - + -
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Residues in contact with ILE 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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18A LEU* 3.3 24.2 - - + -
24A TYR* 3.5 26.0 - - + +
53B ARG* 3.0 27.5 + - + +
54B VAL* 3.6 8.7 - - - +
56B THR* 1.3 76.2 - - - +
58B LEU* 1.3 54.1 + - + +
60B LEU* 3.2 3.8 + - - +
61B TYR* 2.7 42.8 + - + +
64B SER* 4.5 7.6 - - - +
69B VAL* 4.0 26.7 - - + -
72B ARG* 4.1 22.4 - - - +
73B THR* 4.2 11.2 - - + -
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Residues in contact with LEU 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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54B VAL* 2.9 37.4 + - + +
57B ILE* 1.3 76.6 - - - +
59B ALA* 1.3 61.7 + - - +
61B TYR 4.1 3.1 - - - +
62B PRO* 3.1 26.0 - - - +
64B SER* 3.9 24.2 - - - +
69B VAL* 4.5 11.0 - - + -
93B ILE* 3.8 24.7 - - + -
107B LEU* 3.7 39.0 - - + +
108B ALA* 4.1 8.1 - - - +
109B LEU* 3.9 24.2 + - + +
114B ARG* 5.3 0.5 + - - -
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Residues in contact with ALA 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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12A HIS 5.4 2.3 - - - +
13A PRO 5.7 0.4 - - - +
14A VAL* 4.1 13.1 - - + +
55B ILE 3.1 14.8 + - - +
56B THR 3.6 4.3 - - - +
57B ILE 3.2 0.2 - - - -
58B LEU* 1.3 78.3 - - - +
60B LEU* 1.3 61.3 + - - +
62B PRO* 3.8 9.8 - - - +
109B LEU* 3.9 15.7 - - + +
114B ARG* 4.7 10.9 + - - +
117B TYR* 3.4 40.4 - - + +
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Residues in contact with LEU 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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14A VAL* 3.9 32.7 - - + +
16A LEU 4.9 0.9 - - - +
17A ASN* 4.8 10.1 - - - +
18A LEU* 4.0 35.0 - - + +
19A GLU* 4.2 9.2 - - + +
56B THR 3.4 9.1 + - - +
57B ILE* 3.2 7.0 + - - +
59B ALA* 1.3 81.8 - - - +
61B TYR* 1.3 99.3 + - + +
62B PRO* 3.4 7.4 - - - +
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Residues in contact with TYR 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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19A GLU* 2.8 33.8 + - - +
57B ILE* 2.7 31.4 + - + +
58B LEU* 3.5 6.5 - - - +
60B LEU* 1.3 108.0 - - + +
62B PRO* 1.3 66.2 - - - +
63B GLY 3.4 0.2 + - - -
64B SER* 2.7 40.2 + - - +
72B ARG* 3.0 44.4 + - - +
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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