Contacts of the helix formed by residues 38 - 60 (chain A) in PDB entry 2FE2
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 THR 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LYS* 3.3 15.6 + - - +
37A ALA* 1.3 81.6 - - + +
39A GLY* 1.3 54.0 + - - -
41A PRO* 2.8 16.1 - - - +
42A VAL* 2.7 43.5 + - - +
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Residues in contact with GLY 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 5.7 5.0 - - - +
36A LYS* 2.6 41.4 + - - -
38A THR* 1.3 72.5 + - - +
40A PRO* 1.3 67.0 - - - +
42A VAL* 3.8 8.6 - - - +
43A SER* 2.9 25.3 + - - -
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Residues in contact with PRO 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA 4.9 5.2 - - - +
36A LYS 2.8 23.3 - - - +
37A ALA* 2.8 16.6 - - - +
39A GLY* 1.3 77.8 - - - +
41A PRO* 1.3 69.7 - - + +
43A SER* 2.9 22.5 + - - +
44A GLU* 3.0 17.3 - - + +
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Residues in contact with PRO 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA 2.8 29.2 - - - +
38A THR* 2.8 14.3 - - - +
40A PRO* 1.3 83.4 - - + +
42A VAL* 1.3 64.5 + - + +
44A GLU* 2.9 20.1 + - + +
45A LEU* 3.1 17.6 + - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 5.7 7.0 - - + -
28A ALA* 5.9 7.4 - - + -
38A THR* 2.7 33.9 + - - +
39A GLY* 3.2 9.4 + - - +
41A PRO* 1.3 72.0 - - + +
43A SER* 1.3 65.1 + - - +
45A LEU* 2.9 29.7 + - + +
46A ILE* 3.0 24.0 + - + +
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 4.4 16.4 - - - -
28A ALA* 6.1 4.0 - - - -
39A GLY 2.9 14.4 + - - -
40A PRO* 2.9 20.3 + - - +
42A VAL* 1.3 77.5 - - - +
44A GLU* 1.3 62.1 + - - +
46A ILE* 2.7 38.4 - - - +
47A THR* 2.9 17.7 - - - +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO* 3.0 22.1 + - + +
41A PRO* 2.9 14.3 + - + +
42A VAL 2.9 0.6 - - - -
43A SER* 1.3 80.9 + - - +
45A LEU* 1.3 61.8 + - + +
47A THR* 2.6 37.3 + - - +
48A LYS* 3.4 19.2 + - - +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO 3.1 16.4 + - - +
42A VAL* 2.9 23.1 + - + +
44A GLU* 1.3 75.9 - - + +
46A ILE* 1.3 66.0 + - + +
48A LYS* 2.7 44.8 - - + +
49A ALA* 2.9 11.5 + - - +
97A GLN* 3.8 14.6 - - - +
98A THR 5.9 2.0 - - - +
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Residues in contact with ILE 46 (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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21A LYS* 3.1 34.0 - - + +
22A LYS* 5.3 0.7 - - - -
24A THR* 4.9 8.5 - - + -
25A LYS* 2.9 54.7 - - + +
42A VAL* 3.4 20.9 - - + +
43A SER* 2.7 33.9 - - - +
45A LEU* 1.3 83.4 - - + +
47A THR* 1.3 64.0 + - + +
49A ALA* 4.3 0.2 - - - -
50A VAL* 2.8 31.0 + - + +
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 4.4 20.2 - - + +
43A SER* 2.9 18.1 + - - +
44A GLU* 2.6 33.4 + - - +
46A ILE* 1.3 80.3 - - + +
48A LYS* 1.3 64.9 + - - +
50A VAL* 2.7 29.5 - - - +
51A ALA* 3.1 8.1 + - - +
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Residues in contact with LYS 48 (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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44A GLU* 3.4 21.3 - - - +
45A LEU* 2.7 39.0 - - + +
47A THR* 1.3 82.4 + - - +
49A ALA* 1.3 61.5 + - - +
51A ALA* 3.3 7.6 + - - +
52A ALA* 3.2 17.0 + - - +
97A GLN* 3.1 44.7 + - + +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 3.0 33.7 - - + -
45A LEU 2.9 6.2 + - - +
46A ILE* 3.7 1.3 - - - +
48A LYS* 1.3 76.7 - - - +
50A VAL* 1.3 61.9 + - - +
52A ALA* 3.2 4.6 + - - +
53A SER* 3.0 24.8 + - - +
94A THR* 4.8 1.0 - - - +
97A GLN* 2.8 38.7 - - - +
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 4.3 5.8 - - + +
21A LYS* 3.2 37.9 - - + +
22A LYS* 4.4 9.0 - - + +
46A ILE* 2.8 21.1 + - + +
47A THR* 2.7 30.1 - - - +
49A ALA* 1.3 75.3 - - - +
51A ALA* 1.3 63.3 + - + +
53A SER* 3.1 4.3 + - - -
54A LYS* 2.7 54.1 + - - +
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Residues in contact with ALA 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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47A THR 3.1 8.6 + - - +
48A LYS* 3.7 9.4 - - - +
49A ALA 3.2 0.2 - - - -
50A VAL* 1.3 83.6 - - + +
52A ALA* 1.3 63.1 + - - +
54A LYS* 3.1 23.2 + - - +
55A GLU* 3.4 12.5 + - - +
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Residues in contact with ALA 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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48A LYS 3.2 10.1 + - - +
49A ALA 3.6 6.3 - - - +
50A VAL 3.2 0.2 - - - -
51A ALA* 1.3 78.6 - - - +
53A SER* 1.3 56.9 + - - +
55A GLU* 3.0 21.1 + - - +
90A VAL* 2.7 29.8 - - - +
93A GLY* 3.3 12.3 - - - +
94A THR* 3.2 40.4 - - + +
97A GLN* 4.6 0.4 - - + -
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 2.9 14.2 - - - +
17A SER* 4.3 4.4 + - - -
18A PRO* 3.0 40.5 - - - +
21A LYS* 3.9 4.5 + - - -
49A ALA* 3.0 14.1 + - - +
50A VAL* 3.1 4.7 + - - -
52A ALA* 1.3 74.2 - - - +
54A LYS* 1.3 59.0 + - - +
56A ARG* 3.0 3.9 + - - +
57A ASN 2.8 24.8 + - - -
90A VAL* 4.3 2.5 - - - -
94A THR* 4.2 12.1 - - - +
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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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18A PRO* 3.5 22.8 + - + +
22A LYS* 5.7 6.7 - - - +
50A VAL* 2.7 59.7 + - - +
51A ALA* 3.1 11.6 + - - +
53A SER* 1.3 75.6 - - - +
55A GLU* 1.3 63.8 + - + +
57A ASN* 3.2 10.0 + - + +
58A GLY* 3.0 21.5 + - - -
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Residues in contact with GLU 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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51A ALA* 3.7 8.0 - - - +
52A ALA* 3.0 25.7 + - - +
54A LYS* 1.3 79.8 - - + +
56A ARG* 1.3 58.4 + - - +
58A GLY 3.3 0.2 + - - -
59A LEU* 2.7 42.7 + - + +
89A LEU* 2.8 36.7 - - - +
90A VAL* 3.2 16.2 - - + -
93A GLY* 4.6 5.4 - - - -
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Residues in contact with ARG 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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10A THR* 4.5 5.3 + - - +
13A PRO* 6.3 0.4 - - - +
14A VAL* 3.1 36.5 - - + +
53A SER* 3.0 8.9 + - - +
55A GLU* 1.3 75.2 - - - +
57A ASN* 1.3 63.1 + - - +
59A LEU* 3.3 2.8 + - - +
60A SER* 3.1 20.1 + - - -
87A LYS* 2.9 58.9 - - - +
90A VAL* 2.8 42.0 - - + +
91A SER* 3.9 13.2 + - - +
94A THR* 5.5 1.6 - - + +
152A LYS* 4.1 19.0 - - - +
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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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11A PRO* 3.5 33.2 + - - +
14A VAL* 3.1 23.1 - - + +
15A GLU* 4.1 14.3 - - - +
18A PRO* 5.8 1.1 - - + -
53A SER 2.8 6.2 + - - +
54A LYS* 3.3 15.2 - - + +
56A ARG* 1.3 75.8 - - - +
58A GLY* 1.3 66.4 + - - +
60A SER* 3.1 19.8 + - - +
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Residues in contact with GLY 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 LYS 3.0 11.5 + - - -
55A GLU 4.0 0.7 - - - -
57A ASN* 1.3 84.2 + - - +
59A LEU* 1.3 58.1 + - - +
60A SER 3.4 1.0 + - - -
61A LEU* 2.8 29.8 + - - +
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Residues in contact with LEU 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 GLU* 2.7 34.8 - - + +
56A ARG 3.7 3.6 - - - +
57A ASN 3.1 0.4 - - - -
58A GLY* 1.3 77.1 - - - +
60A SER* 1.4 55.1 + - - +
61A LEU* 2.7 27.9 + - + +
82A ILE* 5.0 0.2 - - + -
83A LYS* 3.0 19.0 - - - +
86A LEU* 2.9 83.5 - - + +
87A LYS* 3.7 4.4 - - - +
89A LEU* 5.5 1.6 - - + -
90A VAL 5.1 0.2 - - - +
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU 3.5 2.9 + - - -
10A THR* 2.6 27.9 + - - -
11A PRO* 2.8 39.2 - - - +
14A VAL* 5.2 1.6 - - - -
56A ARG 3.1 12.9 + - - -
57A ASN* 3.1 10.5 + - - +
58A GLY 4.2 0.7 - - - -
59A LEU* 1.4 73.9 - - - +
61A LEU* 1.3 58.2 + - - +
62A ALA 3.4 1.1 + - - +
83A LYS* 5.0 0.7 - - - -
87A LYS* 4.1 16.9 + - - +
209A ALA 4.1 8.4 + - - -
210A ALA* 6.0 0.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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