Contacts of the helix formed by residues 43 - 52 (chain M) in PDB entry 5D4D
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 GLY 43 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28M ARG 4.8 0.4 - - - -
29M ALA* 3.9 13.9 - - - -
42M VAL* 1.3 72.7 - - - +
44M ILE* 1.3 55.0 - - - -
45M GLN 3.0 4.0 - - - -
46M ALA* 2.5 36.5 + - - +
47M ALA 3.5 2.1 + - - -
341M THR* 3.8 24.6 + - - -
345M ARG* 4.8 2.9 + - - +
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Residues in contact with ILE 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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29M ALA 3.1 24.1 + - - +
30M LEU* 4.0 10.3 - - + +
43M GLY* 1.3 70.1 - - - -
45M GLN* 1.3 64.0 + - - +
47M ALA* 3.1 10.1 + - - +
48M PHE* 3.0 35.7 + - + +
71M TYR* 3.8 25.8 - - + +
73M LEU* 5.8 0.2 - - + -
94M LEU* 4.1 4.0 - - + -
118M ILE* 3.6 21.1 - - + -
340M MET* 4.9 4.9 - - + -
341M THR* 3.6 14.6 - - + +
344M PHE* 3.6 42.2 - - + -
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Residues in contact with GLN 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M GLN* 4.8 4.5 - - - +
36M PRO 4.5 6.2 + - - +
39M ARG* 3.5 35.6 + - - +
40M GLU 3.2 23.9 + - - +
41M ASN* 3.5 11.2 - - - +
42M VAL 4.2 2.5 - - - +
43M GLY 3.0 0.4 - - - -
44M ILE* 1.3 83.7 - - - +
46M ALA* 1.3 54.8 + - - +
48M PHE* 3.3 6.3 + - - +
49M ARG* 2.8 40.7 + - + +
68M PHE* 4.0 14.6 - - - -
71M TYR* 3.5 34.0 - - + +
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Residues in contact with ALA 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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41M ASN* 2.7 39.0 + - - +
42M VAL* 4.3 1.6 - - - -
43M GLY 2.5 19.2 + - - +
45M GLN* 1.3 68.4 - - - +
47M ALA* 1.3 59.5 + - - +
49M ARG* 3.8 1.1 - - - -
50M GLU* 2.9 37.8 + - - +
288M ARG* 5.9 1.6 - - - +
345M ARG* 3.3 24.9 - - - +
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Residues in contact with ALA 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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43M GLY 3.5 2.4 + - - +
44M ILE* 3.1 15.1 + - - +
46M ALA* 1.3 79.4 - - - +
48M PHE* 1.3 64.5 + - - +
50M GLU* 3.8 0.8 - - - -
51M THR* 3.0 29.8 + - - +
341M THR 4.6 1.6 - - - +
344M PHE* 3.6 25.8 - - + -
345M ARG* 3.7 33.4 - - + +
348M LEU* 3.4 8.1 - - + -
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Residues in contact with PHE 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 ILE* 3.0 32.9 + - + -
45M GLN 3.5 9.0 - - - +
47M ALA* 1.3 78.7 - - - +
49M ARG* 1.3 58.4 + - - +
52M PHE* 3.0 51.7 + + - +
68M PHE* 3.5 35.4 - + + +
71M TYR* 3.5 36.6 - + + -
94M LEU* 4.1 7.0 - - + -
96M ALA* 4.2 6.5 - - + -
115M LEU* 3.4 33.7 - - + -
344M PHE* 4.2 4.7 - + - -
348M LEU* 3.4 24.6 - - + +
351M LEU* 5.9 0.4 - - + -
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Residues in contact with ARG 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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41M ASN* 3.5 47.1 - - - +
45M GLN* 2.8 32.2 + - + +
46M ALA 3.8 4.0 - - - +
47M ALA 3.2 0.2 - - - -
48M PHE* 1.3 72.8 - - - +
50M GLU* 1.3 67.0 + - + +
52M PHE* 2.6 22.8 - - - +
68M PHE* 4.8 10.8 - - + -
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Residues in contact with GLU 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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41M ASN* 5.7 0.2 - - - +
46M ALA* 2.9 22.7 + - + +
47M ALA* 3.9 2.2 - - - +
49M ARG* 1.3 81.7 - - + +
51M THR* 1.3 62.2 + - + +
52M PHE 3.1 11.1 + - - +
168M ARG* 4.7 4.9 + - - -
264M PRO* 4.7 14.6 - - + +
265M ARG* 3.2 42.8 + - + +
268M ASP* 4.0 5.0 - - - +
288M ARG* 2.8 31.5 + - - -
345M ARG* 3.4 27.8 + - + -
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Residues in contact with THR 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 ALA* 3.0 20.0 + - - +
50M GLU* 1.3 78.6 - - + +
52M PHE* 1.3 66.3 + - - +
53M PRO 4.0 4.0 - - - +
54M ILE* 3.6 19.1 - - - +
265M ARG* 4.4 10.1 + - - +
345M ARG* 4.3 7.4 - - + +
348M LEU* 3.7 32.9 + - + +
349M ALA* 3.9 31.2 - - + +
352M ALA* 4.2 11.2 - - - +
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Residues in contact with PHE 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 PHE* 3.0 52.4 + + - +
49M ARG* 2.6 26.6 - - - +
50M GLU 3.1 4.5 - - - +
51M THR* 1.3 92.0 - - - +
53M PRO* 1.3 65.7 - - + +
54M ILE* 3.6 16.6 - - + -
66M LEU* 3.3 37.7 - - + -
67M ASP* 4.0 11.4 - - - -
68M PHE* 3.6 26.7 - + + +
348M LEU* 4.7 5.4 - - + -
351M LEU* 4.3 19.3 - - + -
352M ALA* 6.4 1.3 - - + -
355M VAL* 6.3 0.4 - - + -
373M VAL* 5.8 3.4 - - + -
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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