Contacts of the helix formed by residues 43 - 56 (chain M) in PDB entry 2GTL
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 ASP 43 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41M ASP 3.8 2.4 + - - -
42M VAL* 1.3 72.2 - - - +
44M LYS* 1.3 56.1 + - - +
45M LYS* 4.1 12.3 - - + +
46M THR* 2.7 42.5 + - - +
47M ILE 3.7 1.7 + - - -
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Residues in contact with LYS 44 (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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42M VAL 3.3 5.2 + - - -
43M ASP* 1.3 70.7 - - - +
45M LYS* 1.3 58.1 + - - +
46M THR 2.9 5.9 + - - -
47M ILE* 3.3 11.3 + - - +
48M ARG* 3.0 32.9 + - + +
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Residues in contact with LYS 45 (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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43M ASP* 2.9 10.9 + - + +
44M LYS* 1.3 78.0 - - - +
46M THR* 1.3 58.8 + - - +
48M ARG* 3.9 10.4 - - - +
49M GLN* 3.6 22.3 + - - +
200M ASP* 5.1 8.7 - - + +
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Residues in contact with THR 46 (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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42M VAL* 4.5 13.6 - - + +
43M ASP* 2.7 29.7 + - - +
45M LYS* 1.3 71.6 - - - +
47M ILE* 1.3 67.2 + - - +
48M ARG 3.0 1.1 - - - -
49M GLN* 2.8 20.1 + - + +
50M LEU* 3.1 16.3 + - + +
47N VAL* 3.9 27.8 - - + -
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Residues in contact with ILE 47 (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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42M VAL* 4.4 24.5 - - + +
43M ASP 3.7 3.1 + - - +
44M LYS* 3.3 12.5 + - - +
46M THR* 1.3 79.1 - - - +
48M ARG* 1.3 65.4 + - + +
50M LEU* 2.8 19.8 + - + +
51M LYS* 2.9 40.0 + - + +
46N PHE* 5.8 7.6 - - + -
47N VAL* 5.2 10.5 - - + -
47O ALA* 6.1 4.9 - - + -
50O LEU* 4.9 13.7 - - + -
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Residues in contact with ARG 48 (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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44M LYS* 3.0 32.1 + - + +
45M LYS* 3.9 10.3 - - - +
47M ILE* 1.3 81.1 - - + +
49M GLN* 1.3 55.3 + - - +
51M LYS* 3.5 11.0 + - - +
52M ALA* 3.0 27.5 + - - +
98M GLU* 4.0 29.7 + - - +
199M GLY* 3.4 32.8 + - - +
200M ASP* 4.8 8.9 - - + +
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Residues in contact with GLN 49 (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 3.6 11.9 + - - +
46M THR* 2.8 13.4 + - - +
48M ARG* 1.3 79.4 - - - +
50M LEU* 1.3 59.5 + - + +
52M ALA* 3.3 1.4 - - - +
53M ARG* 2.9 50.6 + - + +
198M LEU* 3.9 39.5 - - + +
199M GLY* 5.0 0.4 - - - -
200M ASP* 4.5 8.6 + - - +
203M HIS* 4.3 26.2 + - - -
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Residues in contact with LEU 50 (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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46M THR* 3.1 19.7 + - + +
47M ILE* 2.8 14.3 + - + +
49M GLN* 1.3 76.5 - - + +
51M LYS* 1.3 65.3 + - - +
52M ALA 2.8 6.1 + - - -
53M ARG* 3.0 19.9 + - + +
54M ILE* 2.8 33.5 + - + +
47N VAL* 4.3 23.3 - - + -
50N ILE* 3.5 37.5 - - + +
51N ASP* 4.0 19.1 - - + +
54N VAL* 4.9 2.9 - - + -
50O LEU* 4.6 11.9 - - + -
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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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47M ILE* 2.9 30.0 + - + +
48M ARG* 3.8 13.0 - - - +
50M LEU* 1.3 74.6 - - - +
52M ALA* 1.3 55.6 + - - +
54M ILE* 3.9 8.4 - - - +
55M SER* 2.9 31.8 + - - -
46O LYS* 4.6 23.6 - - - +
50O LEU* 4.0 21.5 - - + -
53O ARG* 4.2 20.6 + - - +
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Residues in contact with ALA 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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48M ARG 3.0 13.6 + - - +
49M GLN 3.3 9.2 - - - +
50M LEU 2.8 1.2 + - - -
51M LYS* 1.3 73.9 - - - +
53M ARG* 1.3 67.9 + - - +
54M ILE 3.0 0.9 - - - -
55M SER* 2.8 18.2 + - - -
56M ASN* 2.9 19.7 + - - +
197M ASN 4.0 6.3 - - - +
198M LEU* 3.5 30.5 - - - +
199M GLY* 3.7 7.0 - - - +
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Residues in contact with ARG 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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49M GLN* 2.9 39.4 + - + +
50M LEU* 3.7 21.5 - - + +
52M ALA* 1.3 72.0 - - - +
54M ILE* 1.3 64.3 + - + +
56M ASN* 3.3 19.4 + - - +
57M LEU* 3.4 15.5 - - - +
198M LEU* 4.6 17.0 - - + +
51N ASP* 3.5 35.5 + - - +
54N VAL* 4.1 12.2 - - + +
55N THR* 3.3 24.4 + - - -
58N GLU* 3.0 34.6 + - - +
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Residues in contact with ILE 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 LEU* 2.8 29.4 + - + +
51M LYS* 3.9 3.4 - - - +
53M ARG* 1.3 69.9 - - - +
55M SER* 1.3 54.9 + - - +
56M ASN 2.7 4.9 + - - -
57M LEU* 2.7 35.4 + - - +
58M GLU* 3.3 27.6 + - - +
50N ILE* 4.0 7.9 - - + -
54N VAL* 3.8 20.4 - - + -
50O LEU* 3.8 28.0 - - + +
53O ARG* 4.1 17.0 - - + +
54O VAL* 3.4 23.6 - - + -
57O LEU* 4.4 10.3 - - + -
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Residues in contact with SER 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 2.9 18.2 + - - -
52M ALA* 2.8 9.6 + - - -
54M ILE* 1.3 76.1 - - - +
56M ASN* 1.3 62.3 + - - +
57M LEU 3.3 0.4 + - - -
58M GLU* 3.7 11.3 + - - +
60M HIS* 3.0 41.6 + - - -
68M GLU* 4.8 3.6 + - - -
53O ARG* 3.5 20.9 + - - +
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Residues in contact with ASN 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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52M ALA* 2.9 18.3 + - - +
53M ARG* 3.4 13.9 - - - +
54M ILE 2.7 5.3 + - - -
55M SER* 1.3 82.5 + - - +
57M LEU* 1.3 64.8 + - + +
58M GLU 4.1 4.2 - - - +
60M HIS* 5.1 5.5 + - - -
197M ASN* 3.3 43.3 + - - +
198M LEU* 4.9 3.6 - - - +
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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