Contacts of the helix formed by residues 45 - 57 (chain A) in PDB entry 1XCJ
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 GLU 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A MET* 3.8 11.7 - - + +
42A GLU 3.3 11.7 - - - +
43A ARG 2.8 1.0 + - - -
44A TRP* 1.3 103.1 - - + +
46A THR* 1.3 65.0 + - - +
47A PRO* 3.3 1.8 - - - -
48A TYR* 2.8 18.2 + - + +
49A MET* 2.9 30.0 + - + +
170A LEU* 3.1 20.2 - - + +
213A LEU* 4.2 3.6 - - - -
221A TYR* 2.7 22.6 + - - +
227A MET* 5.3 0.9 - - + -
237A NMG 2.9 36.2 + - - -
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Residues in contact with THR 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 4.7 0.2 + - - -
43A ARG* 2.5 36.7 + - - +
45A GLU* 1.3 75.5 - - - +
47A PRO* 1.3 72.9 - - + +
49A MET 3.2 0.3 + - - -
50A HIS* 2.9 62.2 + - + +
72A ILE* 3.6 22.2 - - + +
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Residues in contact with PRO 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP 3.4 10.8 - - - +
45A GLU 3.3 5.4 - - - -
46A THR* 1.3 96.4 - - + +
48A TYR* 1.3 55.6 + - - +
50A HIS* 3.6 9.3 + - + +
51A SER* 3.2 22.3 + - - -
211A MET* 3.8 23.1 - - + +
213A LEU* 4.0 17.0 - - + -
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Residues in contact with TYR 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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45A GLU* 2.8 15.2 + - - +
47A PRO* 1.3 72.6 - - - +
49A MET* 1.3 76.5 + - + +
50A HIS 3.1 1.6 - - - -
51A SER* 2.8 20.7 + - - -
52A LEU* 3.0 23.6 + - + +
167A TYR 3.9 0.5 + - - -
168A CYS* 3.0 33.5 - - + +
170A LEU* 3.6 25.1 - - + -
173A TRP* 3.6 5.4 - - - -
211A MET* 4.0 8.7 - - + +
213A LEU* 4.0 6.2 - - + +
227A MET* 3.6 44.6 - - + -
228A ILE 2.7 28.6 + - - -
229A THR* 3.4 24.7 - - - -
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Residues in contact with MET 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MET* 3.4 18.6 - - + -
45A GLU* 2.9 34.9 + - + +
46A THR 3.6 6.3 - - - +
48A TYR* 1.3 99.7 - - + +
50A HIS* 1.3 58.2 + - - +
52A LEU* 3.1 20.0 + - + +
53A ALA* 2.8 28.6 + - - +
72A ILE* 3.6 16.8 - - + -
73A ALA* 3.9 11.2 - - + +
132A LEU* 6.2 0.2 - - - -
134A ASP* 3.4 11.4 - - - +
168A CYS* 4.0 2.9 - - - -
236A SAH 3.1 43.5 - - - +
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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
----------------------------------------------------------
46A THR* 2.9 45.0 + - + +
47A PRO* 3.6 8.7 - - + +
49A MET* 1.3 77.1 - - - +
51A SER* 1.3 63.6 + - - +
53A ALA* 3.7 0.5 - - - +
54A ALA* 2.9 26.3 + - - +
72A ILE* 3.6 21.5 + - + +
75A SER* 5.9 0.8 - - - -
76A ARG* 3.5 42.5 + - + +
79A GLN* 5.6 1.1 - - - -
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO 3.2 13.7 + - - -
48A TYR* 2.8 16.9 + - - -
50A HIS* 1.3 78.6 - - - +
52A LEU* 1.3 59.5 + - - +
54A ALA* 3.6 4.8 + - - +
55A ALA* 3.2 21.1 + - - +
209A GLU* 4.9 5.0 + - - +
211A MET* 4.1 12.3 - - - -
229A THR* 2.6 30.6 + - - +
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Residues in contact with LEU 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 TYR* 3.0 35.8 + - + +
49A MET* 3.5 24.0 - - + +
51A SER* 1.3 73.9 - - - +
53A ALA* 1.3 59.0 + - - +
55A ALA* 3.1 5.3 + - - +
56A ALA* 2.8 25.8 + - - +
73A ALA* 5.6 0.4 - - + -
132A LEU* 3.8 24.0 - - + -
134A ASP* 5.1 0.2 - - - +
166A THR* 3.5 31.4 - - + +
167A TYR 4.0 9.9 - - - +
168A CYS* 3.6 32.3 - - + -
229A THR* 3.7 15.7 - - + -
230A PRO* 4.1 1.6 - - + -
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Residues in contact with ALA 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 MET 2.8 13.4 + - - +
52A LEU* 1.3 74.2 - - - +
54A ALA* 1.3 67.0 + - - +
56A ALA* 3.1 2.6 + - - +
57A ALA* 3.0 26.9 + - - +
73A ALA* 3.4 27.6 - - - +
76A ARG* 3.5 25.4 - - + -
77A VAL* 3.8 9.6 - - + +
132A LEU* 3.7 11.4 - - + +
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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 HIS 2.9 17.9 + - - +
51A SER* 3.9 5.4 - - - +
53A ALA* 1.3 76.6 - - - +
55A ALA* 1.3 61.1 + - - +
57A ALA* 3.7 2.8 + - - -
58A SER* 3.2 21.5 + - - -
76A ARG* 3.8 29.2 - - - +
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Residues in contact with ALA 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 SER 3.2 11.2 + - - +
52A LEU* 3.1 10.0 + - - +
53A ALA 3.0 0.8 - - - -
54A ALA* 1.3 81.1 - - - +
56A ALA* 1.3 60.6 + - - +
58A SER* 2.7 28.9 + - - -
164A ILE* 3.4 14.0 - - + +
166A THR* 4.3 11.2 - - - +
229A THR* 4.5 1.6 - - + -
231A LEU* 3.8 29.2 - - + -
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Residues in contact with ALA 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 LEU 2.8 15.3 + - - +
53A ALA* 3.1 5.3 + - - +
55A ALA* 1.3 77.5 - - - +
57A ALA* 1.3 58.4 + - - +
58A SER 3.4 0.4 + - - -
59A ARG 4.8 0.5 + - - -
60A GLY 5.2 0.3 - - - +
63A VAL* 3.9 15.6 - - + +
77A VAL* 5.1 1.1 - - + -
129A ASP 4.7 0.7 - - - +
130A GLY* 3.2 24.8 + - - -
131A ILE 4.1 9.4 - - - +
132A LEU* 3.6 31.9 - - + -
164A ILE* 4.1 7.9 - - - +
166A THR* 4.0 8.2 - - + +
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Residues in contact with ALA 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 ALA 3.0 15.3 + - - +
54A ALA* 3.9 3.1 - - - +
56A ALA* 1.3 75.7 - - - +
58A SER* 1.3 54.7 + - - +
59A ARG 2.9 5.8 - - - -
60A GLY* 2.7 25.1 + - - +
63A VAL* 4.2 5.6 - - + -
77A VAL* 4.5 9.6 - - + +
80A ALA* 3.5 21.7 - - + +
81A PRO* 5.5 1.9 - - - +
82A ILE* 3.2 29.4 - - + +
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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