Contacts of the helix formed by residues 48 - 63 (chain V) in PDB entry 2AXT
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 THR 48 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34V LEU* 4.7 2.0 - - - +
46V THR 4.6 4.9 - - - +
47V LEU* 1.3 77.9 - - - +
49V GLU* 1.3 64.0 + - - +
50V LYS* 2.9 15.3 + - - +
51V GLN* 2.9 32.0 + - - +
52V TYR* 3.0 21.8 + - - +
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Residues in contact with GLU 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ARG* 2.9 49.3 + - - +
29V LEU* 4.0 27.1 - - + +
34V LEU* 4.5 10.2 - - + +
47V LEU 4.1 0.2 + - - -
48V THR* 1.3 73.6 - - - +
50V LYS* 1.3 59.1 + - - +
52V TYR* 4.1 7.2 - - - -
53V LEU* 2.9 31.6 + - + +
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Residues in contact with LYS 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48V THR* 2.9 12.2 - - - +
49V GLU* 1.3 80.7 - - + +
51V GLN* 1.3 65.8 + - + +
53V LEU* 3.7 12.1 + - + +
54V GLU* 3.2 25.7 + - + +
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Residues in contact with GLN 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45V ILE* 5.6 1.9 - - - +
47V LEU* 3.2 32.5 - - + +
48V THR* 2.9 39.8 + - - +
50V LYS* 1.3 77.2 - - + +
52V TYR* 1.3 55.3 + - - +
54V GLU* 2.8 8.8 + - - +
55V GLY* 2.5 36.3 + - - -
136V LYS* 5.7 3.4 + - - +
139V VAL* 4.5 13.5 - - - +
140V ALA* 4.1 15.2 - - + +
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Residues in contact with TYR 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LYS 5.0 1.0 + - - -
311A GLY* 5.5 2.1 - - - -
45F ARG* 5.8 1.1 - - - -
29V LEU* 3.8 24.2 - - + -
34V LEU* 4.3 10.3 - - + -
47V LEU* 5.2 4.6 - - + +
48V THR 3.0 12.8 + - - +
49V GLU* 3.9 7.9 - - - +
51V GLN* 1.3 75.0 - - - +
53V LEU* 1.3 80.6 + - + +
55V GLY* 2.7 24.0 + - - +
56V LYS* 2.8 35.7 + - - +
140V ALA 6.1 0.4 - - - -
143V GLY 6.5 0.4 - - - -
144V HIS* 3.9 18.5 + - - +
147V VAL* 3.9 31.4 - - + -
148V GLU* 3.0 26.7 + - - -
151V ILE* 3.2 21.5 - - + +
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Residues in contact with LEU 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ARG* 3.4 30.1 - - - +
49V GLU* 2.9 29.4 - - + +
50V LYS* 3.8 12.3 - - + +
51V GLN 3.3 0.4 - - - -
52V TYR* 1.3 98.3 - - + +
54V GLU* 1.3 60.4 + - + +
56V LYS* 2.9 15.3 + - - +
57V ARG* 2.8 26.8 + - - +
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Residues in contact with GLU 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50V LYS* 3.2 13.2 + - + +
51V GLN* 2.8 14.3 + - - +
53V LEU* 1.3 77.9 - - + +
55V GLY* 1.3 58.1 + - - +
57V ARG* 2.9 52.4 + - - +
58V LEU* 2.9 40.5 + - + +
137V ASP* 5.8 0.2 - - - +
140V ALA* 4.5 4.5 - - + -
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Residues in contact with GLY 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51V GLN 2.5 17.6 + - - -
52V TYR* 2.7 8.5 + - - -
54V GLU* 1.3 71.6 - - - +
56V LYS* 1.3 56.3 + - - -
58V LEU* 3.2 4.1 + - - +
59V PHE* 2.7 29.5 + - - +
140V ALA* 3.5 31.8 - - - +
141V ILE* 4.0 4.0 - - - -
144V HIS* 4.1 7.6 - - - -
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Residues in contact with LYS 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ILE* 5.3 8.7 - - - +
40J LEU* 4.3 40.2 + - + +
52V TYR* 2.8 43.5 + - - +
53V LEU* 3.3 14.4 - - - +
55V GLY* 1.3 76.4 - - - +
57V ARG* 1.3 64.5 + - - +
59V PHE* 2.9 12.3 + - - +
60V GLN* 2.9 34.4 + - + +
144V HIS* 3.9 21.1 + - + +
148V GLU* 3.9 11.0 + - - -
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Residues in contact with ARG 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53V LEU 2.8 12.0 + - - +
54V GLU* 2.9 46.5 + - - +
55V GLY 3.2 0.2 - - - -
56V LYS* 1.3 77.6 - - - +
58V LEU* 1.3 83.3 + - - +
60V GLN* 3.4 10.5 + - - +
61V TYR* 3.0 37.9 + - - +
137V ASP* 5.7 1.0 + - - -
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Residues in contact with LEU 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V GLU* 2.9 30.0 + - + +
55V GLY 3.7 0.4 - - - +
57V ARG* 1.3 97.4 - - - +
59V PHE* 1.3 65.3 + - - +
61V TYR* 3.4 14.5 - - + +
62V ALA* 3.1 22.7 + - - +
63V CYS* 4.1 2.3 - - - -
132V ASN* 6.4 0.2 - - + -
133V LEU* 4.1 22.9 - - + -
137V ASP* 3.5 42.4 - - + +
140V ALA* 4.5 4.0 - - + -
141V ILE* 3.4 25.3 - - + +
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Residues in contact with PHE 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55V GLY 2.7 20.5 + - - +
56V LYS* 2.9 5.6 + - + +
58V LEU* 1.3 74.2 - - - +
60V GLN* 1.3 59.7 + - + +
63V CYS* 2.6 72.6 + - + +
64V ALA* 3.0 16.1 + - + -
67V HIS* 3.9 26.5 - - + -
68V VAL* 5.1 1.6 - - - -
69V GLY 5.5 1.1 - - - -
80V LEU* 4.0 5.6 - - + -
141V ILE* 4.2 7.6 - - + +
144V HIS* 3.3 31.2 - + + +
145V ILE* 3.6 31.0 - - + -
156V TRP* 3.9 21.8 - + - -
552V HEM 5.3 0.7 - - + -
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Residues in contact with GLN 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C SER* 3.7 27.3 - - - -
417C VAL* 4.7 11.0 + - - +
509C DGD 3.6 25.9 + - - -
39J SER 5.3 0.4 + - - -
40J LEU* 3.8 20.0 - - - +
56V LYS* 2.9 29.5 + - + +
57V ARG* 3.9 7.1 - - - +
59V PHE* 1.3 79.4 - - + +
61V TYR* 1.3 64.0 + - - +
63V CYS 4.2 2.1 + - - -
64V ALA* 3.7 22.7 + - + +
65V SER* 4.6 4.0 + - - -
129V LYS* 5.0 1.7 + - - -
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Residues in contact with TYR 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ILE* 5.6 7.0 - - + +
78C GLU 4.4 6.8 + - - -
79C LYS* 4.1 36.3 - - + +
57V ARG* 3.0 28.3 + - + +
58V LEU* 3.4 18.2 - - + +
59V PHE 3.1 0.2 - - - -
60V GLN* 1.3 80.2 - - - +
62V ALA* 1.3 65.6 + - + +
129V LYS* 2.8 78.6 + - + +
132V ASN* 3.1 26.9 + - + -
133V LEU* 4.2 15.3 - - + -
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Residues in contact with ALA 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58V LEU 3.1 9.2 + - - +
60V GLN 4.7 0.2 - - - -
61V TYR* 1.3 91.6 - - + +
63V CYS* 1.3 60.1 + - - +
65V SER* 5.3 3.4 - - - -
119V PRO* 5.4 1.6 - - - +
129V LYS* 4.0 22.2 - - + +
130V MET* 4.5 8.3 - - - -
133V LEU* 4.9 5.4 - - + -
141V ILE* 5.7 0.2 - - + -
552V HEM 3.0 46.7 - - + +
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Residues in contact with CYS 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58V LEU 4.1 1.6 - - - -
59V PHE* 2.6 70.2 + - + +
60V GLN 4.2 0.2 + - - -
61V TYR 3.8 0.4 - - - -
62V ALA* 1.3 73.5 - - - +
64V ALA* 1.3 69.5 + - - +
65V SER* 2.6 7.4 + - - -
66V CYS* 2.6 15.8 + - - +
67V HIS* 3.1 10.8 + - + +
141V ILE* 3.7 13.7 - - - -
552V HEM 3.1 37.0 - - + +
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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