Contacts of the helix formed by residues 40 - 57 (chain A) in PDB entry 3SMZ
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A MET 4.2 0.2 + - - -
39A LEU* 1.4 74.7 - - - +
41A PRO* 1.4 69.5 - - + +
42A GLU* 2.9 20.3 + - + +
43A GLU* 2.9 51.3 + - - +
44A ILE* 3.2 9.4 + - - +
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Residues in contact with PRO 41 (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 MET* 6.2 2.5 - - + -
39A LEU 3.7 2.4 - - - +
40A ASP* 1.4 86.0 - - + +
42A GLU* 1.4 56.8 + - + +
44A ILE* 4.0 14.4 - - + +
45A ARG* 3.2 50.1 + - - +
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Residues in contact with GLU 42 (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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40A ASP* 2.9 11.9 + - + +
41A PRO* 1.4 77.0 - - + +
43A GLU* 1.3 64.4 + - - +
45A ARG* 3.5 25.7 + - - +
46A LYS* 3.2 22.9 + - - +
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Residues in contact with GLU 43 (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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39A LEU* 4.2 19.5 - - + -
40A ASP* 2.9 25.4 + - - +
42A GLU* 1.3 71.3 - - - +
44A ILE* 1.4 60.2 + - - +
46A LYS* 3.3 27.7 + - - +
47A ARG* 2.9 72.4 + - - +
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Residues in contact with ILE 44 (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 MET* 4.1 11.7 - - + -
39A LEU* 3.3 26.9 - - + +
40A ASP 3.2 8.8 + - - +
41A PRO* 4.0 11.4 - - + +
43A GLU* 1.4 74.5 - - - +
45A ARG* 1.4 57.8 + - + +
47A ARG* 3.3 6.4 + - - +
48A LEU* 2.9 53.4 + - + +
167A GLU 4.0 10.8 - - - +
168A ARG 3.8 11.0 - - - +
169A THR 3.4 31.6 - - - +
170A GLY* 3.8 9.4 - - - -
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Residues in contact with ARG 45 (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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41A PRO* 3.2 46.9 + - - +
42A GLU* 3.5 33.2 + - - +
43A GLU 3.4 0.2 - - - -
44A ILE* 1.4 76.7 - - + +
46A LYS* 1.4 55.4 + - - +
48A LEU* 3.9 4.2 - - - +
49A GLU* 3.0 54.4 + - - +
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Residues in contact with LYS 46 (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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42A GLU 3.2 10.8 + - - +
43A GLU* 3.5 29.6 + - - +
45A ARG* 1.4 76.7 - - - +
47A ARG* 1.3 57.4 - - + +
49A GLU* 4.0 5.4 - - - +
50A HIS* 3.1 30.2 + - + +
53A ARG* 5.0 1.4 + - - -
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Residues in contact with ARG 47 (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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39A LEU* 3.5 26.2 - - - +
43A GLU* 2.9 41.3 + - - +
44A ILE* 3.7 4.5 - - - +
46A LYS* 1.3 74.7 - - + +
48A LEU* 1.4 65.8 + - + +
50A HIS* 3.2 6.3 + - - +
51A THR* 3.1 26.0 + - - -
141A PRO 5.6 1.6 + - - -
144A THR* 5.1 15.3 - - - +
165A TYR* 3.7 46.4 + - + +
170A GLY* 3.0 28.8 + - - +
171A GLN* 4.3 8.9 + - - +
172A SER* 4.3 3.6 - - - +
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Residues in contact with LEU 48 (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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44A ILE* 2.9 35.5 + - + +
45A ARG* 4.1 3.4 - - - +
47A ARG* 1.4 72.3 - - - +
49A GLU* 1.3 58.1 + - + +
51A THR* 3.6 7.0 + - - +
52A GLU* 3.0 30.6 + - - +
165A TYR* 4.0 30.1 - - + +
166A SER 4.1 2.0 - - - +
167A GLU* 3.7 53.8 - - + +
170A GLY* 5.2 0.9 - - - -
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Residues in contact with GLU 49 (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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45A ARG* 3.0 42.3 + - - +
46A LYS* 4.1 5.0 - - - +
48A LEU* 1.3 75.7 - - + +
50A HIS* 1.3 59.2 + - - +
52A GLU* 3.7 6.3 - - + +
53A ARG* 3.0 45.7 + - - +
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Residues in contact with HIS 50 (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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46A LYS* 3.1 21.8 + - + +
47A ARG* 3.2 5.8 + - - +
49A GLU* 1.3 75.5 - - - +
51A THR* 1.4 58.3 + - - +
53A ARG* 3.3 31.5 + - - +
54A GLN* 2.9 59.5 + - + +
145A GLN* 3.7 38.2 - - + +
149A GLU* 3.8 10.7 + - - -
165A TYR* 5.9 1.3 - - + -
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Residues in contact with THR 51 (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 ARG 3.1 10.4 + - - -
48A LEU* 3.8 7.2 - - + +
50A HIS* 1.4 75.5 + - - +
52A GLU* 1.4 53.5 + - - +
54A GLN* 3.3 1.9 + - - +
55A PHE* 2.8 34.3 + - - +
145A GLN* 4.8 1.2 + - - -
162A PHE* 3.8 24.8 - - + +
163A LEU 2.6 29.8 + - - +
164A VAL* 4.7 7.2 - - + -
165A TYR* 3.3 21.5 - - + +
218A LEU* 4.6 13.5 - - + -
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Residues in contact with GLU 52 (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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48A LEU 3.0 18.2 + - - +
49A GLU* 3.7 8.7 - - - +
50A HIS 3.4 0.2 - - - -
51A THR* 1.4 75.2 - - - +
53A ARG* 1.4 56.3 + - - +
55A PHE* 3.3 6.5 + - - +
56A ARG* 2.9 77.7 + - + +
215A PRO* 4.0 16.3 - - - +
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS 5.0 1.4 + - - -
49A GLU* 3.0 49.2 + - - +
50A HIS* 3.3 41.1 - - - +
52A GLU* 1.4 71.3 - - - +
54A GLN* 1.3 69.7 + - + +
56A ARG* 3.6 4.4 + - - +
57A ASN* 3.2 24.3 + - - +
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Residues in contact with GLN 54 (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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50A HIS* 2.9 44.0 + - + +
51A THR 3.6 3.6 - - - +
53A ARG* 1.3 80.3 - - + +
55A PHE* 1.4 62.2 + - - +
57A ASN* 3.2 14.7 + - - +
149A GLU* 5.7 0.6 + - - -
159A GLU 4.5 2.1 - - - +
160A ARG* 3.1 31.3 - - - +
161A CYS* 2.9 39.4 + - - +
162A PHE* 3.7 18.4 - - + -
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR 2.8 19.7 + - - +
52A GLU* 3.7 7.2 - - - +
54A GLN* 1.4 72.3 - - - +
56A ARG* 1.4 79.8 + - + +
57A ASN 3.2 1.4 + - - -
58A ARG* 4.0 6.0 - - - +
160A ARG* 3.0 42.6 + - - +
162A PHE* 3.8 27.9 - + + -
210A ALA 5.6 1.1 - - - -
213A LEU* 3.5 42.6 - - + -
214A THR* 3.8 9.0 - - - -
215A PRO* 3.8 28.3 - - + -
218A LEU* 3.9 21.5 - - + -
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Residues in contact with ARG 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 GLU* 2.9 51.4 + - - +
53A ARG* 3.8 4.9 - - - +
55A PHE* 1.4 84.5 - - + +
57A ASN* 1.3 54.3 + - - +
58A ARG* 2.9 15.3 + - - +
103A GLY* 3.3 21.9 - - - -
104A GLU 6.0 0.4 - - - +
107A GLU* 4.8 19.2 + - - -
215A PRO* 3.5 26.0 - - - +
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Residues in contact with ASN 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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53A ARG 3.2 17.7 + - - +
54A GLN* 3.2 17.4 + - - +
55A PHE 3.2 0.4 - - - -
56A ARG* 1.3 72.3 - - - +
58A ARG* 1.3 58.7 + - - +
59A ARG* 3.8 31.4 + - - +
102A ASN* 5.0 2.6 - - - +
103A GLY* 4.6 6.7 + - - +
159A GLU* 3.5 20.4 + - - +
160A ARG* 3.4 17.3 - - + +
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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