Contacts of the helix formed by residues 37 - 55 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLU 4.3 1.5 + - - +
34A ILE* 3.1 18.8 + - + +
35A ARG 3.8 0.7 - - - +
36A GLN* 1.3 77.5 - - - +
38A PRO* 1.3 74.7 - - - +
39A PHE* 3.0 32.5 + - - +
40A ASN* 3.0 28.5 + - - +
41A SER* 3.8 2.4 + - - -
208A ASP* 2.8 31.1 + - - -
209A VAL* 3.8 1.6 - - - +
210A MET* 3.5 29.4 - - + +
236A ASN* 3.5 7.4 + - - -
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Residues in contact with PRO 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN 3.2 7.8 - - - +
37A ASN* 1.3 85.4 - - - +
39A PHE* 1.3 64.8 + - - +
40A ASN 3.1 0.2 - - - -
41A SER* 3.2 6.8 + - - +
42A ASP* 2.8 31.7 + - - +
209A VAL* 4.1 6.3 - - + -
210A MET* 4.3 0.2 - - - -
236A ASN* 3.8 11.0 - - - +
238A SER* 3.5 24.0 - - - +
240A LEU* 3.7 26.9 - - + -
36B GLN* 3.8 37.5 - - + +
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 3.0 20.2 + - - +
38A PRO* 1.3 78.4 - - - +
40A ASN* 1.3 70.6 + - - +
42A ASP* 3.4 5.9 + - - +
43A VAL* 2.9 44.3 + - + +
88A LEU* 4.3 19.5 - - + -
110A VAL* 4.4 21.8 - - + -
208A ASP* 5.8 1.1 - - - +
236A ASN* 3.7 14.0 - - - +
253A ILE* 4.1 17.0 - - + -
255A PRO* 3.8 15.5 - - + -
258A LEU* 3.9 25.1 - - + -
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Residues in contact with ASN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 4.3 19.8 - - - +
34A ILE* 2.7 35.5 + - - +
35A ARG* 3.9 15.3 - - + +
37A ASN* 3.0 20.7 + - - +
39A PHE* 1.3 88.7 - - - +
41A SER* 1.3 62.4 + - - +
43A VAL* 3.3 8.6 - - - +
44A LEU* 3.1 29.0 + - - +
60A MET* 6.2 0.2 - - - +
88A LEU* 4.9 10.3 - - - +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG 5.3 0.4 + - - -
37A ASN 3.8 1.5 + - - -
38A PRO* 3.2 12.1 + - - -
40A ASN* 1.3 79.0 - - - +
42A ASP* 1.3 59.2 + - - +
44A LEU* 3.8 7.0 - - - +
45A ASN* 3.1 28.2 + - - +
35B ARG* 2.9 46.3 + - - +
36B GLN* 4.4 8.5 - - - -
41B SER* 6.5 1.3 - - - -
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Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO* 2.8 20.7 + - - +
39A PHE* 3.8 0.7 + - - +
41A SER* 1.3 74.6 - - - +
43A VAL* 1.3 65.6 + - - +
45A ASN* 3.3 3.6 + - - +
46A GLY 3.0 17.2 + - - -
236A ASN* 4.6 3.3 - - - +
237A THR 4.9 1.9 - - - +
238A SER* 4.9 2.3 - - - -
255A PRO* 3.4 35.4 - - + +
256A ASP* 3.6 12.2 - - - +
35B ARG* 2.8 41.0 + - - +
36B GLN* 2.9 24.5 + - - +
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 2.9 34.0 + - + +
40A ASN* 3.3 16.6 - - - +
42A ASP* 1.3 76.5 - - - +
44A LEU* 1.3 62.1 + - - +
46A GLY 3.1 1.2 + - - -
47A ILE* 2.8 44.5 + - + +
88A LEU* 4.1 28.5 - - + -
110A VAL* 4.8 14.1 - - + -
255A PRO* 3.6 12.9 + - - +
258A LEU* 4.5 4.0 - - + -
259A GLY* 3.5 22.0 - - - +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.5 29.8 - - + -
40A ASN 3.1 16.7 + - - +
41A SER* 3.8 6.7 - - - +
43A VAL* 1.3 85.2 - - + +
45A ASN* 1.3 56.5 + - - +
47A ILE* 3.3 6.9 + - + -
48A ASN* 2.8 58.2 + - - +
58A THR* 4.8 4.0 - - + -
60A MET* 4.3 18.8 - - + -
88A LEU* 6.2 2.2 - - + -
44B LEU* 3.9 27.8 - - + -
60B MET* 4.1 11.2 - - + -
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Residues in contact with ASN 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER 3.1 19.1 + - - +
42A ASP 3.6 5.1 + - - +
43A VAL 3.3 0.2 - - - -
44A LEU* 1.3 75.5 - - - +
46A GLY* 1.3 59.6 + - - +
48A ASN* 3.3 9.0 + - - +
49A GLN* 2.9 48.0 + - - +
256A ASP* 5.1 5.3 - - - +
27B GLN* 5.8 1.0 + - - -
30B SER* 3.8 14.1 + - - -
35B ARG* 3.0 39.2 - - - +
61B THR 5.1 1.2 - - - +
62B VAL* 3.1 25.7 - - - +
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Residues in contact with GLY 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP 3.0 12.4 + - - -
43A VAL 3.1 2.9 + - - -
45A ASN* 1.3 76.0 - - - +
47A ILE* 1.3 62.5 + - - +
49A GLN* 3.1 21.9 + - - +
50A ALA 3.2 8.8 + - - -
256A ASP* 3.5 26.9 - - - +
260A PHE* 3.4 18.6 - - - -
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 5.6 0.2 - - + -
25A LEU* 3.9 33.2 - - + -
43A VAL* 2.8 30.4 + - + +
44A LEU* 3.7 10.3 - - + +
46A GLY* 1.3 71.2 - - - +
48A ASN* 1.3 61.1 + - - +
50A ALA* 3.1 4.2 + - - +
51A CYS* 2.9 44.2 + - - -
58A THR* 4.8 4.0 - - - +
86A ILE* 4.0 25.8 - - + -
88A LEU* 4.0 24.5 - - + -
259A GLY* 3.4 21.5 - - - +
262A ALA* 4.9 1.1 - - + -
263A GLY* 4.4 4.3 - - - +
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Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 2.8 41.1 + - - +
45A ASN* 3.5 10.1 + - - +
47A ILE* 1.3 75.5 - - - +
49A GLN* 1.3 64.6 + - - +
51A CYS* 4.5 3.7 - - - +
52A ASN* 3.0 35.9 + - - +
58A THR* 4.2 17.7 + - - +
27B GLN* 5.5 0.4 - - - +
59B ARG* 6.0 0.5 - - - -
60B MET* 3.5 54.3 + - - +
61B THR 5.6 1.1 + - - +
62B VAL* 5.1 7.0 - - + -
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Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASN* 2.9 36.6 + - - +
46A GLY* 3.1 12.6 + - - +
48A ASN* 1.3 77.0 - - - +
50A ALA* 1.3 62.4 + - - +
52A ASN* 4.5 1.5 - - - +
53A VAL* 3.4 27.5 + - - +
256A ASP* 5.0 5.9 - - - +
260A PHE* 3.7 25.6 - - + +
62B VAL* 3.3 34.7 + - + +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 3.2 5.2 + - - +
47A ILE 3.1 9.3 + - - +
49A GLN* 1.3 79.5 - - - +
51A CYS* 1.3 58.8 + - - +
53A VAL* 3.1 24.5 - - - +
54A ARG* 3.4 12.1 + - - +
260A PHE* 3.8 15.0 - - + +
263A GLY* 3.8 6.5 - - - -
264A ASN* 3.7 44.7 - - - +
267A ILE* 4.3 2.0 - - - -
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Residues in contact with CYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.3 15.3 - - - -
47A ILE* 2.9 38.0 + - - +
48A ASN* 4.3 4.3 - - - +
50A ALA* 1.3 74.6 - - - +
52A ASN* 1.3 61.4 + - - +
54A ARG 3.2 1.4 + - - -
55A GLY 2.9 12.3 + - - -
56A TYR* 2.9 49.9 + - + +
58A THR* 4.5 10.1 - - - +
263A GLY* 4.8 4.9 - - - -
266A ILE* 5.7 0.7 - - - -
267A ILE* 4.0 21.8 - - - -
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Residues in contact with ASN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN* 3.0 26.5 + - - +
49A GLN* 4.5 2.9 - - - +
51A CYS* 1.3 78.6 - - - +
53A VAL* 1.3 65.5 + - + +
54A ARG 3.5 0.3 + - - -
55A GLY* 3.6 7.8 + - - -
56A TYR 4.2 1.6 - - - +
59B ARG* 3.2 38.8 + - - +
60B MET 3.1 26.0 + - - +
62B VAL* 4.8 6.8 - - + +
72B GLU* 4.2 7.5 + - - +
76B MET* 3.9 13.9 - - - +
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLN 3.4 16.3 + - - +
50A ALA* 3.1 20.9 - - - +
52A ASN* 1.3 78.7 - - + +
54A ARG* 1.3 67.8 + - + +
55A GLY 3.4 0.6 + - - -
260A PHE* 5.6 4.5 - - + -
264A ASN* 5.3 2.2 - - - +
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA 3.8 13.5 - - - +
51A CYS 3.2 3.2 + - - +
53A VAL* 1.3 86.6 - - + +
55A GLY* 1.3 62.4 + - - +
56A TYR* 3.7 5.3 - - - -
264A ASN* 3.1 41.0 + - - +
267A ILE* 3.2 36.9 - - + +
268A ASP* 2.6 32.1 + - - +
271A ARG* 3.0 55.6 + - - +
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.9 22.5 - - - +
51A CYS 2.9 6.0 + - - -
52A ASN* 3.6 7.1 + - - -
53A VAL 3.4 3.6 + - - -
54A ARG* 1.3 79.7 - - - +
56A TYR* 1.3 61.8 + - - -
59B ARG* 5.2 7.0 - - - -
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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
------------------------------------------------------------
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