Contacts of the helix formed by residues 37 - 54 (chain B) in PDB entry 3HUU
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 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLU 4.3 1.7 + - - +
34B ILE* 3.0 17.4 + - - +
35B ARG 3.8 1.0 - - - +
36B GLN* 1.3 79.5 - - - +
38B PRO* 1.3 75.8 - - - +
39B PHE* 3.0 31.3 + - - +
40B ASN* 3.0 26.3 + - - +
41B SER* 3.7 3.6 + - - -
208B ASP* 2.8 36.0 + - - +
209B VAL* 3.8 1.5 - - - +
210B MET* 3.5 20.5 - - + +
236B ASN* 3.7 7.1 + - - -
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Residues in contact with PRO 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 3.9 24.7 - - + +
36B GLN 3.4 7.2 - - - +
37B ASN* 1.3 92.8 - - - +
39B PHE* 1.3 60.4 + - - +
41B SER* 3.1 6.0 + - - -
42B ASP* 3.0 29.5 + - - +
209B VAL* 4.0 7.9 - - + -
210B MET* 4.2 0.7 - - - -
236B ASN* 4.0 3.8 - - - +
238B SER* 3.6 27.8 - - - +
240B LEU* 3.5 39.3 - - + -
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 3.0 21.1 + - + +
38B PRO* 1.3 79.3 - - - +
40B ASN* 1.3 73.7 + - - +
42B ASP* 3.4 5.4 + - - +
43B VAL* 3.0 56.6 + - + +
88B LEU* 4.6 18.4 - - + -
110B VAL* 4.5 12.8 - - + -
124B ASN* 5.4 0.4 - - - -
160B ARG* 6.0 0.2 - - - -
208B ASP* 5.6 1.1 - - - +
236B ASN* 3.7 12.6 - - + +
253B ILE* 3.7 32.5 - - + -
255B PRO* 4.0 5.4 - - + -
258B LEU* 4.0 17.3 - - + -
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Residues in contact with ASN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN* 4.2 20.9 - - - +
34B ILE* 2.7 37.9 + - - +
35B ARG* 3.9 15.5 - - - +
37B ASN* 3.0 19.3 + - - +
39B PHE* 1.3 91.2 - - - +
41B SER* 1.3 62.9 + - - +
43B VAL* 4.0 3.3 - - - +
44B LEU* 3.0 27.4 + - - +
88B LEU* 5.2 8.8 - - - +
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 2.9 54.9 + - - +
36A GLN* 3.9 12.2 + - - -
41A SER* 6.5 1.6 - - - -
35B ARG 5.2 1.9 + - - -
37B ASN 3.7 2.9 + - - -
38B PRO* 3.1 12.2 + - - -
40B ASN* 1.3 79.0 - - - +
42B ASP* 1.3 57.1 + - - +
44B LEU* 3.4 8.4 + - - +
45B ASN 3.0 22.7 + - - -
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 2.5 34.6 + - - +
36A GLN* 2.9 24.3 + - - +
38B PRO* 3.0 21.3 + - - +
39B PHE 3.9 0.9 + - - +
41B SER* 1.3 73.4 - - - +
43B VAL* 1.3 66.0 + - - +
45B ASN* 3.2 3.6 + - - +
46B GLY 3.1 17.7 + - - -
236B ASN* 4.5 3.3 - - - +
237B THR 4.7 5.0 - - - +
255B PRO* 3.4 33.9 - - + +
256B ASP* 3.9 16.2 - - + +
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.0 52.7 + - + +
40B ASN* 4.1 3.1 - - - +
42B ASP* 1.3 75.5 - - - +
44B LEU* 1.3 62.6 + - - +
46B GLY 3.2 1.6 + - - -
47B ILE* 3.1 26.0 + - + +
88B LEU* 3.9 27.8 - - + -
110B VAL* 4.8 11.4 - - + -
255B PRO* 3.6 19.7 - - + +
258B LEU* 4.9 2.7 - - + -
259B GLY* 3.4 17.3 - - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 3.9 27.8 - - + -
60A MET* 4.7 6.5 - - + -
25B LEU* 3.4 31.4 - - + -
40B ASN 3.0 19.6 + - - +
41B SER* 3.6 7.9 - - - +
43B VAL* 1.3 76.4 - - - +
45B ASN* 1.3 60.6 + - - +
47B ILE* 3.3 6.5 + - + +
48B ASN* 2.9 56.6 + - - +
58B THR* 5.1 2.5 - - + -
60B MET* 3.9 22.2 - - + -
88B LEU* 6.4 2.0 - - + -
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Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 5.1 2.9 + - - -
30A SER* 3.6 15.3 + - - -
35A ARG* 3.4 41.0 + - - +
60A MET* 5.9 2.0 - - - +
61A THR 5.2 0.2 - - - +
62A VAL* 3.3 22.0 - - - +
64A GLU* 6.4 0.4 - - - -
41B SER 3.0 9.4 + - - +
42B ASP* 3.2 9.4 + - - +
44B LEU* 1.3 77.1 - - - +
46B GLY* 1.3 62.4 + - - +
48B ASN* 3.4 8.6 + - - +
49B GLN* 3.0 47.4 + - - +
256B ASP* 5.4 6.3 - - - +
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Residues in contact with GLY 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 ASP 3.1 10.9 + - - -
43B VAL 3.7 2.9 - - - -
44B LEU 3.2 0.2 - - - -
45B ASN* 1.3 78.8 - - - +
47B ILE* 1.3 62.5 + - - +
49B GLN* 3.2 20.7 + - - +
50B ALA 3.2 9.4 + - - -
256B ASP* 3.7 13.9 - - - +
260B PHE* 3.4 31.9 - - - -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 5.7 0.2 - - + -
25B LEU* 4.1 26.7 - - + -
43B VAL* 3.1 19.8 + - + +
44B LEU* 3.7 8.7 - - - +
46B GLY* 1.3 75.9 - - - +
48B ASN* 1.3 60.0 + - - +
50B ALA* 3.2 2.9 + - - +
51B CYS* 2.9 44.5 + - - -
58B THR* 4.9 2.7 - - - +
86B ILE* 3.8 33.4 - - + -
88B LEU* 4.0 26.2 - - + -
259B GLY* 3.3 21.8 - - - +
262B ALA* 4.6 1.6 - - + -
263B GLY* 4.5 3.6 - - - -
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Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET* 3.8 39.6 + - - +
61A THR 5.5 0.4 + - - -
62A VAL* 4.1 15.9 - - + -
44B LEU* 2.9 47.1 + - - +
45B ASN* 3.8 6.7 + - - +
47B ILE* 1.3 77.9 - - - +
49B GLN* 1.3 57.1 + - - +
51B CYS* 4.5 5.0 - - - +
52B ASN* 3.0 38.5 + - - +
58B THR* 4.0 20.7 - - - +
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Residues in contact with GLN 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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62A VAL* 3.3 30.5 - - + +
64A GLU* 5.8 1.6 + - - -
45B ASN* 3.0 38.3 + - - +
46B GLY* 3.3 13.8 - - - +
47B ILE 3.2 0.2 - - - -
48B ASN* 1.3 78.6 - - - +
50B ALA* 1.3 58.7 + - - +
52B ASN* 4.4 0.9 - - - +
53B VAL* 3.1 30.0 + - - +
256B ASP* 5.7 2.3 - - - +
260B PHE* 4.1 18.6 - - + -
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Residues in contact with ALA 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 GLY 3.2 4.8 + - - +
47B ILE 3.2 7.7 + - - +
49B GLN* 1.3 78.6 - - - +
51B CYS* 1.3 64.3 + - - +
53B VAL* 3.5 5.8 + - - +
54B ARG* 3.4 26.0 + - - +
260B PHE* 3.8 18.6 - - + +
263B GLY* 3.9 6.5 - - - -
264B ASN* 3.7 41.1 - - - +
267B ILE* 5.6 1.3 - - - -
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Residues in contact with CYS 51 (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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23B ILE* 4.5 19.3 - - - -
47B ILE* 2.9 37.0 + - - +
48B ASN* 4.3 4.7 - - - +
50B ALA* 1.3 75.5 - - - +
52B ASN* 1.3 65.9 + - - +
54B ARG* 3.1 8.8 + - - -
56B TYR* 2.9 56.1 + - + +
57B SER 4.8 4.9 - - - +
58B THR* 5.5 3.6 - - - -
263B GLY* 4.7 8.3 - - - -
267B ILE* 4.5 10.1 - - - -
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Residues in contact with ASN 52 (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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59A ARG* 3.3 40.3 + - - +
60A MET 3.1 26.3 + - - +
62A VAL* 3.5 14.3 - - + +
72A GLU* 4.2 8.1 - - - +
76A MET* 4.3 11.2 - - + +
48B ASN* 3.0 22.2 + - - +
49B GLN* 4.4 2.9 - - - +
51B CYS* 1.3 76.8 - - - +
53B VAL* 1.3 64.6 + - + +
54B ARG 3.2 1.0 + - - -
55B GLY* 3.4 10.7 + - - -
56B TYR 4.2 1.3 + - - -
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Residues in contact with VAL 53 (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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49B GLN 3.1 20.2 - - - +
50B ALA* 3.5 6.4 + - - +
51B CYS 3.3 0.6 - - - -
52B ASN* 1.3 77.6 - - + +
54B ARG* 1.3 63.4 + - + +
55B GLY 3.6 0.6 + - - -
260B PHE* 6.1 2.0 - - + -
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Residues in contact with ARG 54 (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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50B ALA 3.4 14.0 + - - +
51B CYS* 3.1 3.1 + - - +
52B ASN 3.1 1.2 - - - -
53B VAL* 1.3 86.4 - - + +
55B GLY* 1.3 63.0 + - - +
56B TYR* 3.3 23.7 - - + -
264B ASN* 3.7 26.6 + - - +
267B ILE* 3.2 34.5 - - + +
268B ASP* 2.8 31.8 + - - +
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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
------------------------------------------------------------
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