Contacts of the helix formed by residues 34 - 47 (chain C) in PDB entry 1XHU
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 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C GLY 4.4 0.8 + - - -
33C ALA* 1.3 78.3 - - - +
35C GLU* 1.3 66.6 + - - +
36C PRO* 3.1 3.4 - - - -
37C PHE* 2.6 35.9 + - - +
38C GLU* 3.4 2.6 + - - +
130C THR* 3.1 36.9 + - - +
173C TRP* 4.3 3.9 - - - +
9L A 5.1 0.4 - - - -
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLY 4.8 1.6 + - - -
31C HIS* 2.9 41.9 - - - +
33C ALA 4.2 0.4 - - - +
34C GLY* 1.3 74.4 - - - +
36C PRO* 1.3 73.2 - - + +
38C GLU* 2.9 36.1 + - - +
39C LYS* 3.9 1.2 + - - +
130C THR* 4.4 0.4 + - - -
26D GLY* 5.0 2.5 - - - -
27D THR* 2.6 48.5 + - + +
8L G 3.1 37.7 + - - +
9L A 5.0 4.6 + - - -
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Residues in contact with PRO 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 4.7 23.6 - - + -
23C PRO* 4.9 14.1 - - + -
31C HIS 4.9 0.4 - - - +
32C ALA 5.1 1.1 - - - -
33C ALA 3.1 18.2 - - - +
34C GLY 3.3 1.1 - - - -
35C GLU* 1.3 96.1 - - + +
37C PHE* 1.3 52.6 + - + +
39C LYS* 2.7 28.8 + - + +
40C LEU* 2.9 15.4 - - + +
180C LEU* 6.3 0.4 - - + -
25D SER* 4.1 24.0 - - - +
26D GLY* 5.1 4.0 - - - -
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Residues in contact with PHE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 6.1 2.0 - - + -
18C GLN* 3.4 17.7 - - + -
20C VAL* 3.4 19.3 - - + -
34C GLY* 2.6 34.0 + - - +
36C PRO* 1.3 75.6 - - + +
38C GLU* 1.3 60.5 + - - +
40C LEU* 2.9 35.3 + - + +
41C VAL* 3.1 16.7 + - - +
128C VAL* 5.4 0.4 - - - -
130C THR* 4.2 3.6 - - + -
171C VAL* 3.9 28.3 - - + -
173C TRP* 3.4 31.0 - + + -
180C LEU* 3.2 35.2 - - + -
182C CYS* 3.7 15.9 - - + -
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Residues in contact with GLU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLY 3.4 2.4 + - - +
35C GLU* 2.9 32.0 + - - +
37C PHE* 1.3 78.0 - - - +
39C LYS* 1.3 57.6 + - - +
41C VAL* 3.1 5.5 + - - +
42C TYR* 3.0 27.9 + - + +
114C ASP* 2.6 39.3 - - + +
115C ILE* 4.7 5.6 - - + +
128C VAL* 3.7 34.4 - - + +
27D THR* 5.2 4.0 - - - +
8L G 3.6 8.5 + - - +
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU 3.9 0.8 + - - +
36C PRO* 2.7 17.9 + - + +
38C GLU* 1.3 81.2 + - - +
40C LEU* 1.3 59.4 + - + +
42C TYR* 4.0 9.9 - - - +
43C LYS* 3.2 28.4 + - - +
25D SER* 5.0 10.5 - - - +
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 5.1 0.3 - - - +
15C LEU* 3.7 12.0 - - + +
18C GLN* 3.1 45.9 + - + +
19C LYS 4.8 0.2 - - - +
20C VAL* 3.9 21.1 - - + -
36C PRO* 2.9 35.2 - - + +
37C PHE* 2.9 33.9 + - + +
39C LYS* 1.3 81.5 - - + +
41C VAL* 1.3 61.8 + - - +
43C LYS* 4.1 4.8 - - - +
44C PHE* 3.4 22.0 + - - +
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 5.3 3.4 - - + -
15C LEU* 3.4 30.1 - - + -
37C PHE 3.5 12.8 - - - +
38C GLU* 3.1 10.2 + - - +
40C LEU* 1.3 76.9 - - - +
42C TYR* 1.3 59.1 + - - +
43C LYS 3.3 0.2 - - - -
44C PHE* 3.3 5.6 + - - +
45C LEU* 2.8 54.5 + - + +
115C ILE* 4.5 4.5 - - + -
126C LEU* 5.0 1.6 - - + -
128C VAL* 4.9 8.1 - - + -
169C LEU* 3.6 27.6 - - + -
171C VAL* 4.1 13.5 - - + -
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Residues in contact with TYR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLU* 3.0 14.8 + - + +
39C LYS* 4.1 9.4 - - - +
41C VAL* 1.3 78.8 - - - +
43C LYS* 1.3 65.0 + - - +
45C LEU* 3.2 2.6 + - - +
46C LYS* 3.1 27.3 + - + +
53C THR* 3.6 38.8 + - + -
54C PHE* 5.1 0.2 - - - -
55C LYS* 4.2 28.7 + - + +
58C GLU* 5.3 4.5 - - - +
115C ILE* 3.6 27.6 - - + +
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C LYS 3.2 17.5 + - - +
40C LEU* 4.1 6.5 - - - +
42C TYR* 1.3 82.7 - - + +
44C PHE* 1.3 60.7 + - - +
46C LYS* 3.4 7.2 + - - +
47C GLU* 3.2 21.5 + - - +
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Residues in contact with PHE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 5.2 13.3 - - + +
14C ILE* 4.3 30.3 - - + -
15C LEU* 5.0 2.2 - - + -
40C LEU 3.4 17.3 + - - +
41C VAL* 3.3 6.4 + - - +
42C TYR 3.2 0.2 - - - -
43C LYS* 1.3 75.1 - - - +
45C LEU* 1.3 59.2 + - - +
46C LYS 3.1 5.2 - - - -
47C GLU* 3.1 28.2 + - - +
48C ASN* 3.6 7.8 + - - +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 3.4 32.1 - - + -
7C ILE* 5.0 0.2 - - + -
11C ILE* 3.6 24.9 - - + -
41C VAL* 2.8 29.0 + - + +
42C TYR* 3.2 6.5 + - - +
44C PHE* 1.3 76.0 - - + +
46C LYS* 1.3 58.1 + - - +
48C ASN* 4.9 2.2 - - - -
49C LEU* 3.3 36.4 + - + +
53C THR* 3.4 16.1 + - + +
115C ILE* 3.4 23.6 - - + -
117C LEU* 4.7 1.8 - - + -
126C LEU* 3.3 31.6 - - + -
169C LEU* 5.9 0.9 - - + -
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C TYR* 3.1 22.6 + - + +
43C LYS* 3.8 7.9 - - - +
44C PHE 3.1 0.4 - - - -
45C LEU* 1.3 76.0 - - - +
47C GLU* 1.3 57.4 + - - +
48C ASN 3.1 8.7 + - - -
49C LEU 3.9 2.0 - - - -
50C SER* 2.9 38.6 - - - +
53C THR* 5.0 7.9 - - + +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LYS 3.2 16.1 + - - +
44C PHE* 3.1 12.1 + - - +
46C LYS* 1.3 75.6 - - - +
48C ASN* 1.3 61.1 + - - +
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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