Contacts of the helix formed by residues 39 - 50 (chain B) in PDB entry 4HXD
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 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ASP* 3.2 6.2 - - + +
38B GLY* 1.3 90.9 + - - +
40B CYS* 1.3 62.0 + - - +
41B PHE 3.2 3.1 - - - -
42B TYR* 3.0 17.1 + - - +
43B HIS* 2.9 43.7 + - + +
58B PHE* 3.7 31.8 - - + -
62B LYS* 4.9 4.6 - - - +
96B ASP* 3.3 18.1 + - - +
97B ASN* 3.1 28.5 - - - +
98B GLU 3.9 4.4 + - - +
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Residues in contact with CYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 4.6 0.2 - - - -
101A 4LJ 1.8 54.8 - - + +
34B GLN* 4.0 3.5 - - + +
35B PRO 3.6 15.7 - - - +
37B ASP* 4.4 0.4 - - - +
38B GLY 4.2 0.2 - - - +
39B ASN* 1.3 76.9 - - - +
41B PHE* 1.3 58.4 + - - +
43B HIS* 3.6 13.7 - - - +
44B SER* 2.7 34.7 + - - -
151B HIS* 3.6 6.1 - - + -
152B PHE* 3.3 37.0 - - - +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 4.0 11.0 - - - +
101A 4LJ 4.7 1.0 - - - -
39B ASN 3.2 0.8 - - - -
40B CYS* 1.3 85.5 - - - +
42B TYR* 1.3 93.5 + + + +
44B SER* 3.2 14.7 - - - -
45B ILE* 3.2 34.4 - - + +
100B GLY* 4.2 3.8 - - - +
101B GLY* 3.2 35.7 - - - -
104B GLU* 3.6 21.3 - - + -
105B ALA* 3.8 19.7 - - + -
108B LEU* 4.5 2.7 - - + -
116B ILE* 5.9 0.4 - - + -
118B LEU* 4.5 4.9 - - + -
144B LEU* 4.0 13.7 - - + -
152B PHE* 3.7 35.2 - + + -
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLY 5.3 0.2 - - - -
39B ASN* 3.0 17.6 + - - +
41B PHE* 1.3 104.5 - + + +
43B HIS* 1.3 65.2 + - - +
45B ILE* 2.9 9.6 + - + +
46B ALA* 2.9 19.4 + - - +
58B PHE* 3.7 21.5 - + + +
61B VAL* 3.7 24.1 - - + +
62B LYS* 3.5 41.5 - - + -
65B LEU* 3.2 30.9 - - + +
93B ALA* 4.5 5.2 + - - +
98B GLU 3.9 17.0 - - - -
99B TRP 4.6 1.7 + - - -
100B GLY* 4.2 6.6 - - - -
104B GLU* 3.4 17.1 - - + +
108B LEU* 4.7 4.7 - - + -
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Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 3.5 20.6 - - + +
35B PRO* 4.3 12.1 - - + +
37B ASP* 2.7 31.5 + - + -
39B ASN* 2.9 35.9 + - - +
40B CYS* 3.6 10.5 - - - +
42B TYR* 1.3 74.1 - - - +
44B SER* 1.3 57.3 + - - +
46B ALA* 3.1 4.7 + - - -
47B GLU* 2.9 26.5 + - - +
53B LYS* 3.4 25.3 + - - +
55B PRO* 3.7 14.1 + - + -
58B PHE* 3.3 38.7 + + - +
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLN* 3.4 7.8 - - - +
40B CYS 2.7 19.9 + - - -
41B PHE 3.2 11.0 - - - -
42B TYR 3.1 0.2 - - - -
43B HIS* 1.3 76.3 - - - +
45B ILE* 1.3 62.5 + - - +
47B GLU* 3.3 11.4 + - - +
48B LEU* 3.4 17.5 + - - +
144B LEU* 3.8 21.5 - - - -
152B PHE* 3.2 23.3 + - - -
153B ASP 3.4 16.3 - - - -
154B ALA* 4.0 7.6 - - - +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.2 59.4 + - + +
42B TYR* 2.9 8.8 + - - +
44B SER* 1.3 77.1 - - - +
46B ALA* 1.3 54.1 + - - +
48B LEU* 3.0 6.9 + - - +
49B PHE* 2.8 48.0 + - + +
50B PHE* 6.0 0.2 - - + -
61B VAL* 3.4 28.7 - - + -
108B LEU* 4.6 10.5 - - + -
112B LEU* 5.4 7.2 - - + -
116B ILE* 5.2 10.1 - - + -
142B LEU* 4.8 12.5 - - + +
144B LEU* 4.0 16.6 - - + -
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B TYR 2.9 11.8 + - - +
43B HIS* 3.1 11.4 + - - +
45B ILE* 1.3 75.8 - - - +
47B GLU* 1.3 60.8 + - - +
50B PHE* 3.5 37.5 + - + +
53B LYS* 3.7 25.6 - - + +
57B SER* 3.9 21.5 - - - -
58B PHE* 4.1 11.4 - - - +
61B VAL* 4.6 0.9 - - + +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 3.5 25.3 - - + +
34B GLN* 4.0 15.8 + - - +
43B HIS 2.9 12.2 + - - +
44B SER 3.6 9.2 - - - +
45B ILE 3.1 0.4 + - - -
46B ALA* 1.3 79.3 - - - +
48B LEU* 1.3 61.1 + - + +
50B PHE 3.8 7.6 - - - +
51B ASP 5.2 0.9 - - - +
53B LYS* 3.8 25.9 + - - +
154B ALA* 3.8 19.1 - - + -
156B ARG* 2.7 50.4 + - - +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 5.3 0.2 - - + -
44B SER 3.4 11.4 + - - +
45B ILE* 3.0 6.4 + - - +
47B GLU* 1.3 81.0 - - + +
49B PHE* 1.3 60.9 + - - +
50B PHE 3.6 2.2 - - - +
142B LEU* 4.1 30.7 - - + +
143B ASN 3.3 42.2 - - - +
144B LEU* 4.4 5.4 - - + -
154B ALA* 4.3 8.7 - - + -
155B LEU 3.4 24.2 - - - +
156B ARG* 3.8 34.3 + - + +
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 2.8 34.0 + - + +
48B LEU* 1.3 76.1 - - - +
50B PHE* 1.3 97.8 + + + +
61B VAL* 6.0 0.9 - - + -
64B HIS* 4.4 9.0 - + - -
112B LEU* 3.6 45.5 - - + -
114B THR* 4.4 12.6 - - + -
142B LEU* 4.6 14.4 - - + -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA* 3.5 38.7 + - + +
47B GLU 3.8 14.9 - - - +
48B LEU 4.5 1.8 - - - +
49B PHE* 1.3 112.0 + + - +
51B ASP* 1.3 67.4 + - - +
52B VAL 3.9 15.4 - - - +
53B LYS 4.9 0.2 + - - -
57B SER* 4.1 28.0 - - - -
60B LYS* 3.8 24.7 - - + -
61B VAL* 4.6 9.9 - - + -
64B HIS* 5.1 6.7 - + - -
156B ARG* 5.2 1.0 + - - -
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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