Contacts of the helix formed by residues 46 - 62 (chain A) in PDB entry 5I7L
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR* 1.3 83.3 + - - +
47A LEU* 1.3 65.4 + - - -
48A CYS 3.4 2.9 + - - -
49A GLY 4.2 1.1 - - - +
50A SER* 3.1 24.8 + - - -
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Residues in contact with LEU 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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46A GLY* 1.3 67.6 - - - -
48A CYS* 1.3 56.7 + - - +
50A SER* 3.0 4.2 + - - -
51A LEU* 2.6 39.2 + - - +
238A LEU* 3.7 25.1 - - + +
241A ASP* 3.5 45.8 - - + +
242A ILE* 4.0 10.3 - - + +
245A MET* 3.5 33.4 - - + -
252A PHE* 3.7 22.2 - - + +
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Residues in contact with CYS 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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46A GLY 3.4 0.8 - - - -
47A LEU* 1.3 78.4 - - - +
49A GLY* 1.3 58.4 + - - +
51A LEU* 3.4 3.8 + - - +
52A THR* 2.8 35.1 + - - +
120A LEU* 4.1 13.9 - - - +
252A PHE* 3.4 23.3 + - - +
253A CYS* 2.0 52.0 - - - -
254A ILE 5.0 0.4 - - - -
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Residues in contact with GLY 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 THR* 3.7 18.9 + - - +
46A GLY 3.6 4.0 + - - -
47A LEU 3.4 0.4 - - - -
48A CYS* 1.3 79.3 - - - +
50A SER* 1.3 60.6 + - - +
52A THR* 2.9 17.2 + - - -
53A ASN* 3.2 16.8 + - - +
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Residues in contact with SER 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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45A THR* 3.8 16.5 + - - +
46A GLY 3.1 21.1 + - - -
47A LEU* 3.0 6.1 + - - -
49A GLY* 1.3 75.6 - - - +
51A LEU* 1.3 59.9 + - - +
53A ASN* 3.5 3.1 + - - +
54A ALA* 2.8 31.2 + - - +
238A LEU* 4.1 21.2 - - - +
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Residues in contact with LEU 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 LEU 2.6 19.9 + - - +
48A CYS* 3.8 3.8 - - - +
50A SER* 1.3 73.8 - - - +
52A THR* 1.3 57.5 + - - +
54A ALA* 3.1 4.1 + - - +
55A LEU* 2.8 49.4 + - + +
120A LEU* 4.0 13.2 - - + -
129A LEU* 3.6 30.5 - - + -
163A ILE* 4.3 15.0 - - + -
175A LEU* 5.9 1.1 - - + -
231A LEU* 5.4 0.4 - - + -
234A LEU* 3.8 28.5 - - + -
238A LEU* 4.2 5.5 - - + +
242A ILE* 3.6 32.1 - - + -
252A PHE* 5.4 2.0 - - + -
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Residues in contact with THR 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 CYS* 2.8 23.3 + - - +
49A GLY* 2.9 19.9 + - - -
51A LEU* 1.3 75.0 - - - +
53A ASN* 1.3 61.0 + - - -
55A LEU* 3.1 10.1 + - - +
56A SER* 3.1 22.8 + - - -
118A LEU* 3.7 22.1 - - + +
120A LEU* 3.6 39.5 - - + +
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Residues in contact with ASN 53 (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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49A GLY 3.2 13.9 + - - +
50A SER* 4.2 2.7 - - - +
52A THR* 1.3 81.7 + - - +
54A ALA* 1.3 59.0 + - - +
56A SER* 4.0 8.3 - - - -
57A ASN* 2.8 49.0 + - - +
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Residues in contact with ALA 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 SER 2.8 19.4 + - - +
51A LEU 3.1 4.5 + - - +
53A ASN* 1.3 76.1 - - - +
55A LEU* 1.3 63.7 + - - +
57A ASN* 3.6 7.0 + - - +
58A GLY* 3.2 20.3 + - - -
230A VAL* 4.4 0.9 - - - +
234A LEU* 3.7 28.2 - - + +
235A ASP* 6.4 0.2 - - + -
238A LEU* 3.9 14.1 - - + -
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Residues in contact with LEU 55 (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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51A LEU* 2.8 51.7 + - + +
52A THR* 4.6 2.2 - - - -
54A ALA* 1.3 72.6 - - - +
56A SER* 1.3 64.1 + - - +
58A GLY* 3.4 0.5 + - - -
59A LEU* 2.9 33.3 + - + +
118A LEU* 3.5 15.0 - - + -
120A LEU* 4.6 4.5 - - + -
131A VAL* 4.1 35.2 - - + -
133A ILE* 6.4 0.7 - - + -
163A ILE* 4.5 3.1 - - + -
227A VAL* 5.6 7.9 - - + -
230A VAL* 4.0 21.9 - - + +
231A LEU* 4.4 19.1 - - + -
234A LEU* 4.6 4.0 - - + -
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Residues in contact with SER 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 THR 3.1 14.1 + - - -
53A ASN* 4.1 10.3 - - - -
55A LEU* 1.3 78.1 - - - +
57A ASN* 1.3 64.7 + - - +
59A LEU* 3.2 3.6 + - - +
60A LEU* 3.1 32.0 + - - +
115A LEU* 3.7 19.5 - - - +
116A LEU 5.4 0.9 + - - -
118A LEU* 3.5 18.9 - - - +
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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 ASN* 2.8 40.3 + - - +
54A ALA* 3.9 6.2 - - - +
55A LEU 3.4 0.2 - - - -
56A SER* 1.3 78.0 - - - +
58A GLY* 1.3 57.8 + - - +
60A LEU* 3.3 7.6 + - - +
61A SER* 2.8 37.3 + - - +
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Residues in contact with GLY 58 (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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54A ALA 3.2 11.5 + - - -
55A LEU 3.8 2.7 - - - -
57A ASN* 1.3 77.2 - - - +
59A LEU* 1.3 55.8 + - - +
61A SER* 4.5 5.2 - - - -
62A GLY* 2.6 35.2 + - - -
230A VAL* 3.6 21.3 - - - +
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Residues in contact with LEU 59 (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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55A LEU* 2.9 30.8 + - + +
56A SER 3.7 3.6 - - - +
58A GLY* 1.3 76.5 - - - +
60A LEU* 1.3 61.2 + - - +
62A GLY 3.4 0.2 + - - -
63A GLY 3.4 2.9 + - - -
64A LEU* 2.9 39.7 + - + +
115A LEU* 4.5 10.1 - - + -
118A LEU* 4.4 15.0 - - + -
133A ILE* 4.1 33.4 - - + -
223A VAL* 5.0 4.5 - - + -
226A LEU* 3.6 29.2 - - + +
227A VAL* 4.1 23.6 - - + -
230A VAL* 3.7 12.5 - - + +
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Residues in contact with LEU 60 (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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56A SER* 3.1 20.3 + - - +
57A ASN* 3.7 9.4 - - - +
59A LEU* 1.3 76.8 - - - +
61A SER* 1.3 55.3 + - - +
62A GLY 3.0 0.2 - - - -
63A GLY* 2.7 28.8 + - - -
64A LEU* 3.7 3.5 + - + +
65A LEU* 3.9 36.8 + - + +
115A LEU* 3.8 26.2 - - + -
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Residues in contact with SER 61 (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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57A ASN* 2.8 24.6 + - - +
58A GLY* 3.6 4.3 - - - -
60A LEU* 1.3 73.7 - - - +
62A GLY* 1.3 57.7 + - - +
63A GLY 3.2 1.7 + - - -
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Residues in contact with GLY 62 (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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58A GLY 2.6 22.9 + - - -
59A LEU 3.8 1.6 - - - -
60A LEU 3.0 0.4 + - - -
61A SER* 1.3 73.3 - - - +
63A GLY* 1.3 58.9 - - - +
64A LEU 3.6 2.0 - - - -
67A ILE* 4.6 4.0 - - - +
226A LEU* 3.8 22.4 - - - +
229A GLU* 5.1 8.0 - - - +
230A VAL* 5.6 0.4 - - - -
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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