Contacts of the helix formed by residues 42 - 58 (chain A) in PDB entry 1FTT
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 PRO 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ARG* 4.7 10.3 - - + +
32A GLU* 3.6 34.5 - - + +
35A ALA* 3.6 17.2 - - + -
40A LEU 4.6 0.2 - - - +
41A THR* 1.3 85.2 - - - +
43A THR* 1.3 62.1 + - - +
45A VAL* 3.6 6.0 - - + +
46A LYS* 3.0 34.7 + - - +
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Residues in contact with THR 43 (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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41A THR* 4.0 7.5 - - - -
42A PRO* 1.3 80.7 - - - +
44A GLN* 1.3 59.7 + - - +
46A LYS* 3.2 13.1 + - + +
47A ILE* 2.9 50.1 + - + +
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Residues in contact with GLN 44 (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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6A VAL 5.4 0.3 - - - +
7A LEU* 3.6 27.2 - - - +
8A PHE* 3.3 55.2 - - + +
40A LEU* 3.5 27.6 - - + +
41A THR* 3.0 29.4 + - - +
43A THR* 1.3 74.3 - - - +
45A VAL* 1.3 62.1 + - - +
47A ILE* 3.4 11.2 + - + +
48A TRP* 3.0 23.4 + - - +
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Residues in contact with VAL 45 (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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16A LEU* 5.0 1.8 - - + -
26A LEU* 5.4 0.7 - - + -
31A ARG* 4.1 20.9 - - + +
34A LEU* 3.4 35.9 - - + -
35A ALA* 4.0 8.1 - - + -
40A LEU* 3.7 25.1 - - + +
41A THR 2.9 19.8 + - - +
42A PRO* 3.6 7.2 - - + +
44A GLN* 1.3 74.8 - - - +
46A LYS* 1.3 64.2 + - - +
48A TRP* 3.1 9.4 + - - +
49A PHE* 2.9 42.0 + - + -
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 4.1 36.7 - - - +
42A PRO* 3.0 27.4 + - - +
43A THR* 3.2 10.0 + - + +
45A VAL* 1.3 73.5 - - - +
47A ILE* 1.3 54.1 + - + +
49A PHE* 3.2 8.8 + - + +
50A GLN* 2.8 37.2 + - + +
53A ARG* 4.8 4.3 + - - +
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Residues in contact with ILE 47 (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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8A PHE* 5.8 4.3 - - + -
43A THR* 2.9 39.0 + - + +
44A GLN* 3.6 9.4 - - + +
46A LYS* 1.3 76.9 - - + +
48A TRP* 1.3 56.9 + - - +
50A GLN* 3.1 7.8 + - - +
51A ASN* 2.9 52.2 + - - +
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Residues in contact with TRP 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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8A PHE* 3.7 33.4 - + + -
13A VAL* 4.2 15.3 - - + +
16A LEU* 3.3 51.3 - - + +
17A GLU* 3.5 15.0 - - + -
20A PHE* 3.6 19.7 - + + -
44A GLN 3.0 13.1 + - - +
45A VAL* 3.4 9.6 - - - +
47A ILE* 1.3 75.8 - - - +
49A PHE* 1.3 91.3 + + - +
51A ASN* 3.2 9.6 + - - +
52A HIS* 2.9 83.5 + + - -
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Residues in contact with PHE 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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16A LEU* 3.8 26.5 - - + -
19A ARG* 4.0 8.7 - - + -
20A PHE* 3.8 29.3 - + - -
23A GLN 4.6 0.4 - - - -
24A LYS 3.9 18.4 - - - -
25A TYR* 4.2 9.0 - + + -
26A LEU* 3.1 34.8 - - + -
34A LEU* 4.7 2.7 - - + -
45A VAL* 2.9 37.4 + - + +
46A LYS* 3.6 8.3 - - - +
48A TRP* 1.3 101.7 - + - +
50A GLN* 1.3 61.8 + - - +
52A HIS 4.0 0.2 + - - -
53A ARG* 3.0 38.8 + - - +
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Residues in contact with GLN 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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46A LYS* 2.8 18.1 + - + +
47A ILE* 3.3 12.1 - - - +
49A PHE* 1.3 71.3 - - - +
51A ASN* 1.3 66.6 + - - +
52A HIS 3.3 0.2 + - - -
53A ARG* 3.3 29.9 + - - +
54A TYR* 2.9 46.5 + - - +
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Residues in contact with ASN 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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8A PHE* 6.3 1.2 - - - -
47A ILE* 2.9 41.2 + - - +
48A TRP* 3.2 9.5 + - - +
50A GLN* 1.3 82.4 - - - +
52A HIS* 1.3 64.7 + - + +
54A TYR* 3.5 11.3 + - - +
55A LYS* 2.9 28.8 + - - +
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Residues in contact with HIS 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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13A VAL* 5.2 2.2 - - + +
17A GLU* 4.2 16.7 + - + +
20A PHE* 3.5 31.3 - + + -
48A TRP* 2.9 72.4 + + + +
49A PHE 4.5 0.2 - - - +
50A GLN 3.2 0.2 - - - -
51A ASN* 1.3 81.6 - - + +
53A ARG* 1.3 62.9 + - - +
55A LYS* 3.5 8.9 - - + +
56A MET* 3.5 23.7 + - - +
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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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20A PHE* 3.8 7.2 - - + -
25A TYR* 3.3 64.6 - - + +
46A LYS* 4.8 5.3 + - - +
49A PHE* 3.0 37.2 + - - +
50A GLN* 3.3 29.0 + - - +
52A HIS* 1.3 74.4 - - - +
54A TYR* 1.3 67.9 + - - +
56A MET* 3.3 12.7 + - + +
57A LYS* 3.1 21.8 + - - +
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Residues in contact with TYR 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 GLN* 2.9 35.0 + - - +
51A ASN* 3.6 10.5 - - - +
52A HIS 3.3 0.2 - - - -
53A ARG* 1.3 76.5 - - - +
55A LYS* 1.3 61.4 + - - +
57A LYS* 3.1 21.9 + - + +
58A ARG* 2.9 60.2 + - + +
62A ASP* 2.8 29.2 + - + -
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Residues in contact with LYS 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 ASN 2.9 17.7 + - - +
52A HIS* 3.5 11.0 - - + +
54A TYR* 1.3 78.7 - - - +
56A MET* 1.3 59.7 + - + +
58A ARG* 3.4 10.3 + - + -
59A GLN* 2.9 60.2 + - - +
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Residues in contact with MET 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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20A PHE* 4.0 30.1 - - + -
24A LYS* 4.0 19.1 - - - +
25A TYR* 4.9 2.2 - - - +
52A HIS 3.5 9.1 + - - +
53A ARG* 3.3 12.9 + - + +
55A LYS* 1.3 77.7 - - + +
57A LYS* 1.3 62.2 + - - +
59A GLN* 3.3 21.4 - - - +
63A LYS* 3.9 4.9 + - - -
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Residues in contact with LYS 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 14.1 + - - +
54A TYR* 3.4 24.7 - - + +
56A MET* 1.3 74.2 - - - +
58A ARG* 1.3 53.7 + - - +
61A LYS 2.8 23.7 - - - +
62A ASP* 4.5 2.7 - - - -
63A LYS* 2.8 65.6 + - + +
64A ALA* 3.9 18.8 + - + +
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Residues in contact with ARG 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 TYR* 2.9 45.3 + - + +
55A LYS* 3.8 11.0 - - + +
57A LYS* 1.3 69.6 - - - +
59A GLN* 1.3 65.5 + - - +
60A ALA 3.0 0.5 + - - -
61A LYS* 3.0 25.6 + - - -
62A ASP* 2.9 45.0 + - - +
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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