Contacts of the helix formed by residues 52 - 72 (chain A) in PDB entry 6FIT
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A LEU 4.5 0.7 - - - +
51A ARG* 1.3 87.8 - - + +
53A ASP* 1.3 56.9 + - - +
55A VAL* 3.3 11.1 + - + +
56A ALA* 3.1 25.6 + - - +
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Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.8 15.4 - - + +
51A ARG* 2.8 48.6 + - - +
52A PRO* 1.3 76.5 - - - +
54A GLU* 1.3 70.9 + - - +
55A VAL 3.1 1.3 - - - -
56A ALA* 3.1 8.6 + - - +
57A ASP* 2.8 25.8 + - - +
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.3 21.1 - - + +
22A SER* 4.9 0.7 + - - -
40A PRO* 5.2 8.3 - - + +
42A ARG* 2.7 58.4 + - - +
50A LEU* 3.0 30.8 - - + +
51A ARG* 2.9 42.9 + - + +
53A ASP* 1.3 76.4 + - - +
55A VAL* 1.3 58.2 - - - +
57A ASP* 3.8 1.8 - - - +
58A LEU* 2.8 31.4 + - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.8 33.2 - - + +
50A LEU* 4.0 21.3 - - + +
51A ARG 3.0 20.1 + - - +
52A PRO* 3.3 10.1 - - + +
53A ASP 3.1 0.2 - - - -
54A GLU* 1.3 78.5 - - - +
56A ALA* 1.3 63.5 + - - +
58A LEU* 3.3 6.2 + - - +
59A PHE* 3.1 28.4 + - + +
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Residues in contact with ALA 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 PRO 3.1 10.8 + - - +
53A ASP* 3.1 9.8 + - - +
55A VAL* 1.3 81.1 - - - +
57A ASP* 1.3 58.3 + - - +
59A PHE* 4.1 1.5 - - - +
60A GLN* 3.1 44.9 + - - +
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Residues in contact with ASP 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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19A THR* 3.1 19.4 + - - -
20A GLU* 3.8 16.8 - - - +
21A LEU* 3.6 26.6 + - + +
22A SER* 2.5 25.6 + - - +
53A ASP 2.8 15.4 + - - +
54A GLU 3.8 2.7 - - - +
56A ALA* 1.3 76.2 - - - +
58A LEU* 1.3 64.2 + - - +
60A GLN* 3.9 10.0 - - - +
61A THR* 2.6 34.7 + - - -
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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
----------------------------------------------------------
22A SER* 3.7 9.1 + - - -
38A VAL* 3.9 16.2 - - + -
39A CYS* 4.0 23.3 - - - -
40A PRO* 4.1 6.1 - - + -
47A PHE* 4.7 0.7 - - + -
50A LEU* 4.1 13.7 - - + -
54A GLU 2.8 18.4 + - - +
55A VAL 3.6 4.3 - - - +
57A ASP* 1.3 77.1 - - - +
59A PHE* 1.3 84.0 + - + +
61A THR* 3.5 3.1 + - - -
62A THR* 2.9 28.4 + - - -
95A VAL* 3.9 28.5 - - + -
97A VAL* 3.8 20.0 - - + -
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Residues in contact with PHE 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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47A PHE* 3.8 25.1 - + - -
55A VAL* 3.1 20.4 + - + +
56A ALA* 4.9 1.3 - - - +
58A LEU* 1.3 97.4 - - + +
60A GLN* 1.3 65.5 + - - +
62A THR* 3.6 15.7 - - + +
63A GLN* 3.1 18.9 + - - +
80A PHE* 5.9 3.4 - + + -
82A MET* 3.8 22.2 - - + -
97A VAL* 3.8 30.1 - - + -
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Residues in contact with GLN 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 ALA* 3.1 34.3 + - - +
57A ASP* 3.9 11.8 - - - +
58A LEU 3.3 0.4 - - - -
59A PHE* 1.3 76.4 - - - +
61A THR* 1.3 57.8 + - - +
63A GLN* 2.6 39.5 + - - +
64A ARG* 3.2 11.8 + - - +
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Residues in contact with THR 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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17A LEU* 3.7 27.1 - - + -
19A THR* 3.6 29.1 + - + +
22A SER* 3.9 4.7 + - - -
23A PHE 5.3 2.5 - - - +
24A ALA* 5.3 1.3 - - + -
38A VAL* 3.9 19.1 - - + -
57A ASP* 2.6 23.5 + - - -
58A LEU 3.6 4.3 - - - -
60A GLN* 1.3 79.2 - - - +
62A THR* 1.3 56.3 + - - -
64A ARG* 3.4 11.8 + - - +
65A VAL* 3.0 36.1 + - + +
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Residues in contact with THR 62 (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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38A VAL* 3.4 24.8 - - - +
58A LEU 2.9 19.9 + - - -
59A PHE* 3.7 17.7 - - + -
60A GLN 3.0 0.4 - - - -
61A THR* 1.3 74.9 - - - +
63A GLN* 1.3 65.6 + - - +
65A VAL* 4.2 0.6 - - - +
66A GLY 3.1 15.1 + - - -
80A PHE* 3.3 37.7 - - + -
97A VAL* 3.5 24.4 - - + +
99A VAL* 4.3 7.1 - - + +
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Residues in contact with GLN 63 (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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59A PHE 3.1 11.5 + - - +
60A GLN* 2.6 27.8 + - - +
62A THR* 1.3 69.3 - - - +
64A ARG* 1.3 67.8 + - + +
66A GLY* 3.1 2.8 + - - -
67A THR* 3.0 23.3 + - - +
80A PHE* 5.2 5.9 - - - -
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Residues in contact with ARG 64 (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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17A LEU* 4.2 12.7 - - + +
19A THR* 4.1 23.0 - - - +
60A GLN* 3.6 16.8 - - - +
61A THR* 3.7 11.4 - - - +
63A GLN* 1.3 77.3 - - + +
65A VAL* 1.3 66.7 + - + +
67A THR* 2.7 20.1 + - - -
68A VAL* 3.1 12.6 + - - +
146A PHE* 4.1 42.2 + - + +
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Residues in contact with VAL 65 (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 PHE* 3.7 22.4 - - + -
17A LEU* 3.7 24.7 - - + -
24A ALA* 4.0 9.9 - - + -
36A VAL* 3.5 29.8 - - + -
38A VAL* 4.0 18.6 - - + -
61A THR* 3.0 21.0 + - + +
62A THR 4.2 0.9 - - - +
64A ARG* 1.3 78.5 - - - +
66A GLY* 1.3 63.0 + - - +
68A VAL* 3.6 0.5 + - - +
69A VAL* 3.2 24.3 + - - +
99A VAL* 4.5 2.5 - - + -
146A PHE* 4.1 9.4 - - + -
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Residues in contact with GLY 66 (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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62A THR 3.1 15.4 + - - -
63A GLN 3.5 4.0 - - - -
64A ARG 2.8 2.6 + - - -
65A VAL* 1.3 78.0 - - - +
67A THR* 1.3 61.3 + - - +
69A VAL* 3.3 3.6 - - - +
70A GLU* 3.1 22.9 + - - +
78A LEU* 3.4 21.0 - - - +
80A PHE* 4.5 2.0 - - - -
99A VAL* 3.9 15.9 - - - +
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Residues in contact with THR 67 (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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63A GLN* 3.0 15.2 + - - +
64A ARG* 2.7 17.0 + - - -
66A GLY* 1.3 69.6 - - - +
68A VAL* 1.3 62.2 + - + +
70A GLU* 3.0 30.3 + - - +
71A LYS* 3.0 26.9 + - + +
78A LEU* 4.2 2.0 - - - +
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Residues in contact with VAL 68 (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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64A ARG 3.1 5.4 + - - +
65A VAL 3.8 4.0 - - - +
67A THR* 1.3 82.0 - - + +
69A VAL* 1.3 63.3 + - + +
71A LYS* 3.2 13.1 + - - +
72A HIS* 3.0 27.0 + - - +
142A LEU* 4.1 21.5 - - + -
145A TYR* 3.9 33.6 - - + +
146A PHE* 3.4 42.8 - - + -
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Residues in contact with VAL 69 (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 PHE* 4.6 1.3 - - + -
34A GLY 3.9 4.9 - - - +
36A VAL* 3.8 30.5 - - + -
65A VAL* 3.2 20.6 + - + +
66A GLY 3.3 9.2 - - - +
68A VAL* 1.3 78.2 - - + +
70A GLU* 1.3 60.8 + - - +
72A HIS* 4.2 0.7 - - - -
73A PHE* 3.2 31.7 + - + -
78A LEU* 4.1 1.1 - - + -
99A VAL* 4.0 19.1 - - + -
101A PRO* 3.3 29.7 - - + +
142A LEU* 4.1 17.9 - - + -
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Residues in contact with GLU 70 (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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66A GLY 3.1 12.3 + - - +
67A THR* 3.0 19.4 + - - +
69A VAL* 1.3 76.9 - - - +
71A LYS* 1.3 62.8 + - - +
74A HIS* 3.3 2.1 + - - -
75A GLY* 3.0 48.3 + - - +
76A THR 3.1 8.2 - - - +
77A SER* 3.0 34.2 - - - +
78A LEU* 4.0 19.4 + - + +
101A PRO* 4.3 7.6 - - - -
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Residues in contact with LYS 71 (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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67A THR* 3.0 25.3 + - + +
68A VAL* 3.2 12.9 + - - +
70A GLU* 1.3 75.6 - - - +
72A HIS* 1.3 63.9 + - - +
74A HIS* 3.1 27.4 + - - -
145A TYR* 3.5 37.4 + - + +
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Residues in contact with HIS 72 (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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68A VAL 3.0 13.3 + - - +
71A LYS* 1.3 80.0 - - - +
73A PHE* 1.3 93.1 + + + +
74A HIS* 3.4 14.7 + - - -
138A GLU* 5.7 2.2 - - - +
141A ALA* 4.1 25.7 - - + +
142A LEU* 4.1 8.2 - - + +
145A TYR* 3.0 41.9 + + + +
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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