Contacts of the helix formed by residues 36 - 54 (chain G) in PDB entry 1FFT
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 ILE 36 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G GLY 3.7 0.4 - - - -
35G GLN* 1.3 72.8 - - - +
37G GLY* 1.3 68.5 + - - +
38G LEU* 3.2 21.3 - - + +
39G GLU* 2.3 90.8 + - + +
40G GLN* 3.2 8.0 - - - +
178G ARG 3.5 7.6 - - - +
179G LEU* 3.1 48.0 - - + +
180G GLY 5.1 0.9 - - - +
195G LEU* 4.8 4.0 - - + -
196G ILE 3.4 19.1 - - - +
198G ASN* 4.2 5.3 - - - +
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Residues in contact with GLY 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G ILE* 1.3 71.7 - - - +
38G LEU* 1.3 65.6 + - - +
40G GLN* 2.8 28.4 + - - +
41G ARG* 3.0 12.5 + - - -
196G ILE* 4.2 7.9 + - - +
198G ASN* 3.6 17.7 + - - +
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Residues in contact with LEU 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G ILE* 3.2 16.2 - - + +
37G GLY* 1.3 72.1 - - - +
39G GLU* 1.3 56.2 + - - +
40G GLN 2.6 12.8 + - - -
41G ARG* 2.7 28.5 + - + +
42G SER* 3.1 14.8 + - - -
113G ALA* 3.7 30.7 - - + -
114G LEU* 4.0 28.9 - - + +
179G LEU 5.8 0.2 - - - +
180G GLY 5.9 2.7 - - - +
181G SER* 6.6 0.2 - - - -
194G HIS 4.0 11.7 - - - +
195G LEU* 4.6 11.4 - - + -
196G ILE* 4.9 11.3 + - + +
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Residues in contact with GLU 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G PRO 5.5 0.4 - - - +
33G LYS 2.5 28.4 - - - +
34G GLY* 2.9 9.0 - - - -
35G GLN 2.8 8.2 + - - -
36G ILE* 2.3 69.4 + - + +
38G LEU* 1.3 71.0 - - - +
40G GLN* 1.3 71.1 + - - +
42G SER* 4.1 4.9 - - - -
43G LEU* 2.3 68.5 + - + +
178G ARG 3.9 2.4 - - - +
179G LEU 4.8 3.6 - - - +
180G GLY* 5.8 1.8 - - - -
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Residues in contact with GLN 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLY* 4.3 10.0 + - - -
36G ILE 3.2 11.0 + - - +
37G GLY* 2.8 21.3 - - - +
38G LEU 2.6 3.6 + - - -
39G GLU* 1.3 106.8 + - - +
41G ARG* 1.3 72.2 + - - +
42G SER 2.6 13.0 + - - -
44G ILE* 2.8 49.7 + - + +
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Residues in contact with ARG 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G GLY* 3.0 20.9 + - - -
38G LEU* 2.7 29.2 + - + +
40G GLN* 1.3 86.6 - - - +
42G SER* 1.3 56.7 + - - -
44G ILE* 4.7 5.8 - - - +
45G LEU* 5.0 3.4 - - - +
110G THR* 4.0 22.4 - - + +
113G ALA* 5.5 6.7 - - + -
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Residues in contact with SER 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405F GLY* 4.1 26.8 + - - +
406F ALA* 4.4 3.1 - - - -
408F PHE* 5.1 3.3 - - - +
409F VAL* 4.7 8.8 - - - +
38G LEU* 3.4 19.5 - - - -
39G GLU* 3.9 3.8 - - - -
40G GLN 2.6 9.1 + - - -
41G ARG* 1.3 76.9 - - - +
43G LEU* 1.3 61.3 + - - +
44G ILE 3.7 0.2 - - - -
45G LEU* 3.6 25.1 - - - +
46G THR* 4.6 2.3 + - - +
114G LEU* 6.0 1.7 - - - +
180G GLY* 4.9 8.1 + - - -
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409F VAL* 3.5 34.8 - - + -
31G ASP* 3.3 34.7 - - + +
32G PRO* 3.9 36.6 - - + +
39G GLU* 2.3 64.0 + - + +
42G SER* 1.3 69.0 - - - +
44G ILE* 1.3 60.3 + - + +
45G LEU 3.0 1.6 - - - -
46G THR* 2.3 31.8 + - + +
47G ALA* 3.8 1.0 + - - +
179G LEU 5.5 0.2 - - - -
180G GLY* 5.1 7.0 - - - +
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Residues in contact with ILE 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G GLN* 2.8 55.3 + - + +
41G ARG* 4.7 4.9 - - - +
43G LEU* 1.3 74.6 - - + +
45G LEU* 1.3 66.6 + - - +
47G ALA* 3.2 6.5 + - + +
48G PHE* 2.7 41.9 + - + +
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Residues in contact with LEU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F LEU* 5.1 3.4 - - + +
403F VAL* 3.9 22.4 - - + -
405F GLY* 4.2 4.0 - - - -
406F ALA* 3.2 47.3 - - + +
40G GLN 3.9 1.8 + - - -
41G ARG* 5.0 1.5 - - - +
42G SER* 3.6 21.7 - - - +
44G ILE* 1.3 81.0 - - - +
46G THR* 1.3 66.1 + - - +
48G PHE* 3.3 8.9 - - - +
49G GLY* 2.9 20.5 + - - -
106G LEU* 6.3 2.7 - - + -
110G THR* 3.3 35.4 - - + +
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Residues in contact with THR 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F LEU* 3.7 24.8 - - + +
406F ALA* 3.6 37.7 - - + +
409F VAL* 6.6 0.2 - - + -
410F LEU* 4.5 7.0 - - + -
476F PHE* 6.0 2.9 - - + -
31G ASP* 3.0 18.2 + - - +
42G SER 4.9 2.9 - - - +
43G LEU* 2.3 32.6 + - + +
45G LEU* 1.3 77.8 - - - +
47G ALA* 1.3 53.2 + - - -
49G GLY 3.2 0.5 + - - -
50G LEU* 2.7 50.9 + - - +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G ASP* 4.4 10.7 + - - +
43G LEU 4.7 0.7 - - - +
44G ILE* 3.2 9.5 + - + +
46G THR* 1.3 78.3 + - - +
48G PHE* 1.3 67.2 + - - +
50G LEU* 3.0 12.7 + - - +
51G MET* 2.9 25.7 + - - +
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Residues in contact with PHE 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G ILE* 2.7 37.2 + - + +
45G LEU* 3.3 8.1 - - - +
47G ALA* 1.3 74.4 - - - +
49G GLY* 1.3 62.2 + - - +
51G MET* 3.3 9.2 + - - +
52G LEU* 3.2 45.6 - - + +
106G LEU* 3.5 43.5 - - + -
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Residues in contact with GLY 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F LEU* 5.1 3.8 - - - -
45G LEU* 2.9 15.8 + - - -
46G THR 3.7 1.6 - - - -
48G PHE* 1.3 74.3 - - - +
50G LEU* 1.3 55.0 + - - +
51G MET 3.0 2.5 - - - -
52G LEU* 2.6 25.6 + - - -
53G ILE* 2.7 19.9 + - - +
103G LEU* 3.5 28.1 - - - +
106G LEU* 5.3 0.4 - - - -
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Residues in contact with LEU 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396F MET* 5.2 9.4 - - + -
397F THR* 6.1 0.4 - - - -
400F LEU* 3.3 42.7 - - + +
476F PHE* 5.4 11.7 - - + -
46G THR* 2.7 39.4 + - - +
47G ALA* 3.0 10.5 + - - +
49G GLY* 1.3 71.6 - - - +
51G MET* 1.3 55.5 + - - +
53G ILE* 2.7 34.5 - - + +
54G VAL* 2.9 18.4 - - - +
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Residues in contact with MET 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ALA 2.9 11.4 + - - +
48G PHE* 3.5 11.0 - - - +
49G GLY 3.0 0.2 - - - -
50G LEU* 1.3 76.5 - - - +
52G LEU* 1.3 71.9 + - + +
53G ILE 3.4 1.6 - - - -
54G VAL* 3.1 24.7 - - + +
55G VAL* 4.5 3.5 - - - +
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Residues in contact with LEU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G PHE* 3.2 57.0 - - + +
49G GLY* 2.6 10.1 + - - +
51G MET* 1.3 95.6 - - + +
53G ILE* 1.3 59.0 + - - +
55G VAL* 3.8 18.9 - - + +
99G ILE* 4.0 9.7 - - - +
102G PHE* 6.0 6.7 - - + -
103G LEU* 3.9 26.4 - - + +
106G LEU* 5.4 0.4 - - + -
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Residues in contact with ILE 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396F MET* 3.4 44.0 - - + +
399F VAL* 4.1 19.3 - - + -
400F LEU* 5.4 1.6 - - + +
1002F HEO 4.0 17.3 - - + -
49G GLY 2.7 5.1 + - - +
50G LEU* 2.7 50.3 - - + +
52G LEU* 1.3 78.3 - - - +
54G VAL* 1.3 57.3 + - + +
55G VAL 2.5 17.3 + - - -
56G ILE* 2.6 27.9 + - + +
57G PRO* 2.8 13.9 - - + +
99G ILE* 4.6 3.6 - - + -
103G LEU* 5.4 4.9 - - + -
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Residues in contact with VAL 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396F MET* 5.8 2.9 - - - -
50G LEU 2.9 20.6 - - - +
51G MET* 3.1 35.7 - - + +
53G ILE* 1.3 84.0 - - + +
55G VAL* 1.3 57.9 + - + +
56G ILE 2.7 11.0 + - - -
57G PRO* 3.1 16.2 - - + -
58G ALA* 3.1 34.5 + - + +
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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