Contacts of the helix formed by residues 48 - 61 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A TYR* 3.7 3.0 - - - -
46A GLY 4.3 0.8 + - - -
47A MSE 1.3 75.7 - - - +
49A ILE* 1.3 67.5 + - - +
50A PRO* 4.0 12.6 - - + -
51A GLU* 3.1 37.1 + - - +
52A TRP 3.1 10.0 + - - -
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Residues in contact with ILE 49 (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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31A ASN 5.4 1.3 - - - +
34A SER* 4.2 28.3 - - - +
35A GLY* 4.5 4.9 - - - +
38A ALA* 3.7 20.2 - - + -
41A TYR* 3.3 21.5 + - - +
48A ALA* 1.3 70.6 - - - +
50A PRO* 1.3 74.7 - - + +
52A TRP* 3.2 5.5 + - - +
53A ARG* 3.1 21.5 + - + +
75A MSE 5.1 7.4 - - + -
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Residues in contact with PRO 50 (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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48A ALA* 3.6 12.1 - - + -
49A ILE* 1.3 96.5 - - + +
51A GLU* 1.3 64.6 + - + +
53A ARG* 3.4 2.6 + - - +
54A VAL* 3.0 27.6 + - + +
75A MSE 3.8 26.0 - - + +
79A ALA* 4.6 15.9 - - + +
80A VAL* 5.9 0.2 - - - -
83A ALA* 4.1 17.0 - - + -
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Residues in contact with GLU 51 (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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46A GLY 4.7 0.7 - - - +
47A MSE 3.5 18.8 - - + +
48A ALA* 3.1 38.2 + - + +
50A PRO* 1.3 77.4 - - + +
52A TRP* 1.3 65.8 + - - +
54A VAL* 3.2 4.9 + - - +
55A ILE* 3.0 26.4 + - - +
83A ALA* 4.0 29.4 - - + +
86A ARG* 3.6 27.7 - - + +
87A LEU* 3.7 18.0 - - + +
90A ARG* 4.3 10.5 + - - -
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Residues in contact with TRP 52 (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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37A ILE* 4.9 0.9 - - + -
41A TYR* 3.3 56.1 - + + +
47A MSE 4.0 16.2 - - - -
48A ALA 3.1 6.1 + - - -
49A ILE 3.2 1.5 + - - +
51A GLU* 1.3 76.3 - - - +
53A ARG* 1.3 69.2 + - - +
55A ILE* 3.0 18.6 + - + +
56A THR* 3.0 41.9 + - + +
116A VAL* 4.4 3.8 - - + -
117A TYR* 3.9 25.6 - + - -
120A VAL* 3.6 40.6 - - + -
121A ALA 3.8 8.5 - - - -
124A VAL* 4.2 7.5 - - + +
802A CL 3.2 29.2 - - + +
16B LEU* 3.8 15.3 - - + -
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Residues in contact with ARG 53 (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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34A SER* 5.6 3.8 + - - -
49A ILE* 3.1 14.0 + - + +
50A PRO 3.6 7.4 - - - +
51A GLU 3.3 0.2 - - - -
52A TRP* 1.3 79.9 - - - +
54A VAL* 1.3 64.0 + - - +
56A THR* 2.7 55.2 + - - +
57A ILE* 3.1 17.4 + - + +
69A VAL* 5.8 0.2 - - + -
73A THR* 4.1 11.0 - - + -
75A MSE 3.8 32.1 - - + -
802A CL 3.1 33.9 - - - +
18B LEU* 3.8 7.9 - - - +
23B PRO* 5.0 2.2 - - - +
24B TYR* 3.6 49.1 - - - +
27B SER* 4.7 7.9 + - - -
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Residues in contact with VAL 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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50A PRO 3.0 18.9 + - - +
51A GLU 3.6 7.9 - - - +
52A TRP 3.2 0.2 - - - -
53A ARG* 1.3 74.7 - - + +
55A ILE* 1.3 64.6 + - - +
57A ILE* 3.2 6.9 + - - +
58A LEU* 2.9 43.8 + - + +
69A VAL* 4.2 14.4 - - + -
75A MSE 5.5 2.0 - - - -
80A VAL* 4.2 22.9 - - + -
83A ALA* 4.0 18.6 - - + -
84A VAL* 4.3 13.2 - - + -
87A LEU* 3.6 19.5 - - + -
93A ILE* 4.9 0.2 - - + -
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Residues in contact with ILE 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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47A MSE 4.4 11.4 - - + -
51A GLU 3.0 19.5 + - - +
52A TRP* 3.0 25.4 + - + +
54A VAL* 1.3 77.1 - - - +
56A THR* 1.3 58.0 + - - +
58A LEU* 3.8 1.4 - - - +
59A ALA* 2.9 28.6 + - - +
87A LEU* 4.0 18.6 - - + -
92A PHE* 4.3 11.2 - - + +
93A ILE* 4.0 14.4 - - + -
109A LEU* 3.5 30.3 - - + +
113A GLY* 4.3 8.3 - - - +
116A VAL* 5.2 2.7 - - + -
117A TYR* 4.1 24.9 - - + +
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Residues in contact with THR 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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52A TRP* 3.0 54.9 + - + +
53A ARG* 2.7 43.3 + - - +
55A ILE* 1.3 75.5 - - - +
57A ILE* 1.3 59.8 + - - +
59A ALA* 3.7 2.1 + - - +
60A LEU* 3.4 21.7 + - - +
117A TYR* 4.1 15.1 + - + -
16B LEU* 4.1 10.4 - - + +
18B LEU* 3.8 17.9 - - - +
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Residues in contact with ILE 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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53A ARG* 3.1 17.3 + - - +
54A VAL 3.6 6.5 - - - +
56A THR* 1.3 76.4 - - - +
58A LEU* 1.3 56.1 + - - +
60A LEU* 3.1 4.0 + - - +
61A TYR* 2.7 37.8 + - + +
64A SER* 4.7 8.7 - - - +
69A VAL* 4.1 31.0 - - + -
72A ARG* 3.6 35.4 - - - +
73A THR* 3.9 20.4 - - + -
18B LEU* 3.5 23.8 - - + -
24B TYR* 3.8 11.2 - - + +
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Residues in contact with LEU 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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54A VAL* 2.9 38.5 + - + +
55A ILE 3.9 2.9 - - - +
57A ILE* 1.3 73.7 - - - +
59A ALA* 1.3 65.2 + - - +
61A TYR 4.0 3.4 - - - +
62A PRO* 3.3 25.6 - - - +
64A SER* 3.8 33.2 - - - +
69A VAL* 4.5 9.6 - - + -
93A ILE* 3.8 25.8 - - + -
107A LEU* 3.8 39.0 - - + +
108A ALA 4.4 0.4 - - - +
109A LEU* 4.0 19.9 + - + +
114A ARG* 4.6 0.7 + - - -
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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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55A ILE 2.9 18.4 + - - +
56A THR 3.8 1.8 - - - +
58A LEU* 1.3 79.4 - - - +
60A LEU* 1.3 61.5 + - - +
62A PRO* 4.0 5.7 - - - +
109A LEU* 3.7 21.5 - - + +
114A ARG* 3.3 21.8 + - - +
117A TYR* 3.6 40.4 - - + -
12B HIS* 4.8 4.2 - - - +
14B VAL* 5.5 3.4 - - - +
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Residues in contact with LEU 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 3.4 12.7 + - - +
57A ILE 3.1 4.3 + - - +
59A ALA* 1.3 81.9 - - - +
61A TYR* 1.3 103.8 + - + +
62A PRO* 3.6 6.0 - - - +
117A TYR* 5.5 1.8 - - - +
14B VAL* 3.7 39.6 - - + +
16B LEU 4.5 6.5 - - - +
17B ASN* 5.3 2.0 - - - +
18B LEU* 4.4 30.7 - - + +
19B GLU* 4.6 7.2 - - - +
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Residues in contact with TYR 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 ILE* 2.7 22.3 + - + +
58A LEU* 3.5 5.6 - - - +
60A LEU* 1.3 117.4 - - + +
62A PRO* 1.3 67.1 - - - +
64A SER* 2.7 39.6 + - - +
72A ARG* 3.3 55.7 + - - +
19B GLU* 4.9 6.2 + - - -
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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