Contacts of the helix formed by residues 51 - 64 (chain D) in PDB entry 4XQ2
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 ASN 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D HIS* 2.8 26.9 + - - +
30D VAL* 5.0 0.6 - - - +
31D SER 4.0 8.5 + - - -
34D TYR* 3.5 9.3 + - - -
47D GLY* 4.2 2.9 - - - +
50D GLU* 1.3 77.8 - - - +
52D PRO* 1.3 72.0 - - - +
53D THR* 2.9 23.4 + - - -
54D ARG* 3.0 37.7 + - + +
55D GLU* 3.0 29.0 + - - +
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Residues in contact with PRO 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 4.0 14.4 - - + -
29D HIS* 3.8 38.1 - - + +
34D TYR* 3.8 13.2 - - + +
44D TYR* 3.6 27.8 - - + +
51D ASN* 1.3 86.4 - - - +
53D THR* 1.3 57.9 + - - +
55D GLU* 3.3 13.6 + - + +
56D GLU* 2.9 39.1 + - + +
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Residues in contact with THR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PRO 3.6 4.4 + - - +
28D ILE* 3.8 14.3 - - + -
29D HIS* 2.8 37.7 + - - -
51D ASN* 2.9 9.8 + - - -
52D PRO* 1.3 77.1 - - - +
54D ARG* 1.3 66.1 + - - +
56D GLU* 3.1 27.1 + - - +
57D LEU* 3.2 12.0 + - - +
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Residues in contact with ARG 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C LEU* 5.0 5.9 - - - +
47D GLY 2.9 32.3 + - - -
48D ARG* 3.2 18.4 + - - +
49D GLY 3.4 17.4 + - - -
50D GLU* 3.4 7.5 - - - +
51D ASN* 3.0 29.7 + - + +
53D THR* 1.3 76.8 - - - +
55D GLU* 1.3 63.8 + - - +
57D LEU* 3.2 11.3 + - + +
58D GLU* 3.1 33.5 + - - +
72D VAL* 3.4 32.0 - - + +
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ARG* 4.2 17.4 + - - +
44D TYR* 2.5 44.4 + - - -
49D GLY 5.3 0.2 - - - +
50D GLU* 4.1 9.0 - - - +
51D ASN 3.0 22.4 + - - +
52D PRO* 3.6 7.5 - - + +
53D THR 3.2 0.2 - - - -
54D ARG* 1.3 78.2 - - + +
56D GLU* 1.3 55.9 + - + +
58D GLU* 3.2 18.3 + - - +
59D GLU* 2.8 29.3 + - - +
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLY 4.3 0.2 - - - +
14D GLY* 3.4 31.4 - - - +
16D ARG* 5.1 7.0 - - + +
26D PRO* 3.7 30.9 - - + +
27D PRO 4.7 1.0 - - - +
29D HIS* 4.1 13.2 + - - -
52D PRO* 2.9 29.7 + - - +
53D THR* 3.3 24.1 + - - +
55D GLU* 1.3 75.9 - - - +
57D LEU* 1.3 61.6 + - - +
59D GLU* 3.3 2.7 + - - +
60D CYS* 3.1 23.7 + - - +
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D THR 3.2 8.3 + - - +
54D ARG* 3.5 10.1 - - - +
56D GLU* 1.3 77.8 - - - +
58D GLU* 1.3 58.5 + - - +
60D CYS* 3.3 10.2 + - + +
61D LEU* 3.0 45.8 + - + +
72D VAL* 3.7 32.1 - - + -
195D THR* 6.0 5.6 - - + +
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ARG* 3.1 23.0 + - - +
55D GLU* 3.2 27.1 + - - +
57D LEU* 1.3 73.5 - - - +
59D GLU* 1.3 64.7 + - - +
61D LEU* 3.3 1.7 + - - -
62D ALA* 2.9 22.6 + - - +
70D ALA* 3.2 39.9 - - - +
71D THR* 3.4 8.9 - - - +
72D VAL* 3.0 44.4 + - + +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLY* 5.1 0.7 - - - -
14D GLY* 3.5 28.4 + - - +
55D GLU 2.8 18.8 + - - +
56D GLU* 3.8 5.4 - - - +
58D GLU* 1.3 72.4 - - - +
60D CYS* 1.3 58.0 + - - +
62D ALA* 3.5 5.8 + - - +
63D GLY* 3.0 25.3 + - - -
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Residues in contact with CYS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ARG* 3.8 19.9 - - - +
10D LEU* 4.1 17.5 - - - -
13D GLY* 3.3 27.2 - - - +
56D GLU 3.1 10.8 + - - +
57D LEU* 3.4 15.7 - - + +
59D GLU* 1.3 77.8 - - - +
61D LEU* 1.3 67.1 + - - +
63D GLY* 3.2 10.0 + - - -
64D LEU* 3.2 23.3 + - - +
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 3.0 34.5 + - + +
58D GLU* 3.9 3.8 - - - +
60D CYS* 1.3 74.8 - - - +
62D ALA* 1.3 66.8 + - - +
64D LEU* 3.1 35.5 + - + +
65D GLU* 3.8 10.0 + - - +
70D ALA* 4.2 9.9 - - + -
71D THR 5.8 0.7 - - - +
72D VAL* 3.6 30.5 - - + -
178D PRO* 5.9 2.5 - - + -
193D TYR* 6.1 8.1 - - + -
195D THR* 4.6 22.9 - - + -
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLU 2.9 16.2 + - - +
59D GLU* 3.8 5.8 - - - +
61D LEU* 1.3 76.2 - - - +
63D GLY* 1.3 63.4 + - - +
65D GLU* 3.1 5.0 + - - +
66D ARG 3.1 3.5 + - - -
67D ALA* 3.0 46.6 + - - +
68D PRO 4.5 2.5 - - - +
69D PHE* 3.8 25.4 - - - +
70D ALA* 3.8 4.8 - - - +
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Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ARG* 2.3 48.9 + - - -
13D GLY* 6.3 1.6 - - - -
59D GLU 3.0 15.4 + - - -
60D CYS* 3.2 5.8 + - - -
62D ALA* 1.3 78.5 - - - +
64D LEU* 1.3 51.7 + - - +
65D GLU 3.1 1.5 + - - -
66D ARG* 3.3 9.5 + - - -
67D ALA 5.2 0.2 - - - -
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Residues in contact with LEU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PHE* 3.1 27.2 - - + -
9D ARG* 3.9 25.4 + - + +
10D LEU* 3.5 42.2 - - + +
60D CYS* 3.2 19.4 + - - +
61D LEU* 3.1 27.9 + - + +
63D GLY* 1.3 76.4 - - - +
65D GLU* 1.3 58.4 + - + +
178D PRO* 3.8 27.1 - - + -
182D GLN* 2.9 24.4 + - - +
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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