Contacts of the helix formed by residues 50 - 64 (chain M) in PDB entry 1T4F
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 MET 50 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26M THR* 2.9 31.2 + - + +
28M VAL* 4.6 7.4 - - + +
49M THR* 1.3 71.9 - - - +
51M LYS* 1.3 58.9 + - + +
53M VAL* 3.2 10.6 + - - +
54M LEU* 2.9 47.8 + - + +
100M TYR* 4.5 14.8 - - + -
103M ILE* 3.9 29.2 - - + -
104M TYR* 3.4 52.5 - - + +
107M LEU* 4.4 9.4 - - + -
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Residues in contact with LYS 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLU* 6.2 8.7 - - + +
26M THR 6.3 0.9 - - - +
49M THR* 3.1 10.3 - - - +
50M MET* 1.3 79.4 - - + +
52M GLU* 1.3 62.7 + - + +
54M LEU* 3.4 10.2 + - + +
55M PHE* 3.0 24.4 + - - +
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Residues in contact with GLU 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M LYS* 3.4 29.2 + - - +
48M TYR* 3.2 23.4 - - + +
49M THR* 3.0 47.4 + - - +
51M LYS* 1.3 72.7 - - + +
53M VAL* 1.3 61.8 + - - +
55M PHE* 3.2 7.6 + - - +
56M TYR* 2.9 46.6 + - + -
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Residues in contact with VAL 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M VAL* 3.8 24.0 - - + -
30M PRO* 5.9 0.9 - - + -
34M LEU* 4.6 15.0 - - + -
38M LEU* 4.3 24.7 - - + +
48M TYR* 3.9 14.8 - - + -
49M THR 3.0 12.3 + - - +
50M MET* 3.5 10.8 - - - +
52M GLU* 1.3 77.2 - - - +
54M LEU* 1.3 63.6 + - - +
56M TYR* 3.3 1.8 + - - +
57M LEU* 2.9 25.9 + - + +
103M ILE* 4.0 29.8 - - + -
107M LEU* 4.8 2.0 - - + -
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Residues in contact with LEU 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M MET* 2.9 32.9 + - + +
51M LYS* 3.7 9.4 - - + +
53M VAL* 1.3 76.6 - - - +
55M PHE* 1.3 63.7 + - - +
57M LEU* 3.4 3.0 + - - -
58M GLY 3.1 9.0 + - - -
99M ILE* 4.7 0.4 - - + -
100M TYR* 3.5 34.5 - - + +
103M ILE* 3.5 28.9 - - + -
23P TRP* 3.0 27.9 + - + +
26P LEU* 4.1 36.1 - - + +
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Residues in contact with PHE 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51M LYS 3.0 17.9 + - - +
52M GLU* 3.2 7.2 + - - +
54M LEU* 1.3 76.5 - - - +
56M TYR* 1.3 88.2 + + - +
58M GLY* 3.1 4.0 + - - -
59M GLN* 3.1 55.3 + - + +
20P MET* 5.3 8.7 - - + -
23P TRP* 4.7 4.7 - - - +
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Residues in contact with TYR 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M LEU* 5.1 0.4 - - - -
38M LEU* 3.6 29.8 - - + -
41M VAL* 3.7 27.0 - - + +
42M GLY* 3.4 22.6 - - - -
43M ALA* 3.5 19.0 + - - +
45M LYS* 5.3 2.5 - - + +
48M TYR* 4.1 26.2 - + - -
52M GLU* 2.9 37.7 + - + +
55M PHE* 1.3 98.0 - + - +
57M LEU* 1.3 58.1 + - - +
59M GLN* 3.1 6.2 + - + +
60M TYR* 2.8 29.0 + - - +
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Residues in contact with LEU 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M LEU* 6.2 4.3 - - + -
37M LEU* 4.6 17.3 - - + -
38M LEU* 4.8 1.5 - - + +
53M VAL* 2.9 20.3 + - + +
54M LEU 3.7 4.0 - - - +
55M PHE 3.3 0.2 - - - -
56M TYR* 1.3 76.0 - - - +
58M GLY* 1.3 62.5 + - - +
60M TYR* 3.2 6.6 + - + +
61M ILE* 2.9 31.8 + - + +
82M LEU* 3.7 35.4 - - + -
86M PHE* 3.9 26.0 - - + -
99M ILE* 4.8 0.2 - - + -
103M ILE* 3.9 18.8 - - + -
23P TRP* 3.6 26.7 - - + -
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Residues in contact with GLY 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M LEU 3.1 10.9 + - - -
55M PHE 3.1 2.9 + - - -
57M LEU* 1.3 77.8 - - - +
59M GLN* 1.3 59.3 + - - +
61M ILE 3.3 0.3 + - - -
62M MET* 2.9 35.3 + - - +
19P PHE* 3.6 8.2 - - - -
20P MET* 5.3 0.2 - - - -
23P TRP* 3.4 34.7 - - - +
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Residues in contact with GLN 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M VAL* 4.6 11.9 - - + -
55M PHE* 3.1 45.5 + - + +
56M TYR* 3.1 10.1 + - + +
58M GLY* 1.3 77.7 - - - +
60M TYR* 1.3 56.2 + - - +
62M MET* 3.6 14.0 - - - +
63M THR* 2.8 33.1 + - - -
20P MET* 3.5 35.6 - - - +
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Residues in contact with TYR 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M LEU* 3.2 44.9 - - + -
40M SER* 3.4 28.0 - - - -
41M VAL* 3.9 9.6 - - + +
56M TYR 2.8 13.8 + - - +
57M LEU* 3.2 12.1 + - + +
59M GLN* 1.3 74.3 - - - +
61M ILE* 1.3 72.6 + - + +
63M THR* 3.0 9.6 - - + +
64M LYS* 3.0 62.6 + - + +
66M LEU* 4.2 8.7 - - + -
80M ASP* 2.7 29.2 + - - -
81M LEU* 3.7 14.5 - - + +
82M LEU* 4.3 3.6 - - + -
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Residues in contact with ILE 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M LEU* 2.9 25.7 + - + +
58M GLY 3.6 3.8 - - - +
60M TYR* 1.3 78.4 - - + +
62M MET* 1.3 59.5 + - - +
64M LYS 3.4 0.7 + - - -
65M ARG* 2.9 23.7 + - - -
66M LEU* 3.1 28.7 + - + -
67M TYR* 4.3 8.1 - - + +
75M VAL* 4.1 12.3 - - + -
82M LEU* 3.8 30.7 - - + -
91M PHE* 4.1 10.8 - - + -
19P PHE* 3.6 24.5 - - + -
23P TRP* 3.8 32.5 - - + -
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Residues in contact with MET 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M GLY 2.9 18.7 + - - +
59M GLN* 3.6 19.3 - - - +
61M ILE* 1.3 77.5 - - - +
63M THR* 1.3 63.0 + - - +
65M ARG* 2.9 30.6 + - - -
67M TYR* 4.0 18.2 - - + +
19P PHE* 3.2 27.6 - - + +
20P MET* 3.3 41.7 - - + +
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Residues in contact with THR 63 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M VAL* 4.1 15.5 - - + -
59M GLN 2.8 19.2 + - - +
60M TYR* 3.0 26.9 - - + +
62M MET* 1.3 73.2 - - - +
64M LYS* 1.3 66.5 + - + +
65M ARG* 3.3 19.6 + - - +
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Residues in contact with LYS 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M TYR* 3.0 49.3 + - + +
63M THR* 1.3 84.6 - - + +
65M ARG* 1.3 72.2 + - - +
66M LEU* 3.2 20.3 + - + +
80M ASP* 2.8 29.6 + - - +
81M LEU* 5.1 2.2 - - - +
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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