Contacts of the helix formed by residues 30 - 44 (chain A) in PDB entry 4ND1
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 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLY 3.4 4.8 + - - -
29A SER* 1.3 75.8 - - - +
31A GLN* 1.3 68.5 + - - +
32A ILE 3.4 1.8 - - - -
33A GLY 3.3 1.4 + - - +
34A GLY 2.9 18.5 + - - -
58A ILE* 5.3 1.1 - - - -
62A LYS* 3.0 15.4 + - - -
97A THR* 4.8 0.6 + - - -
401A NAD 3.3 33.0 + - - -
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Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY* 1.3 72.5 - - - +
32A ILE* 1.3 64.7 + - - +
34A GLY* 4.2 0.3 - - - -
35A ASN* 3.5 23.0 + - - -
62A LYS* 4.0 6.2 + - - +
244A GLY* 5.6 12.0 - - - +
245A THR 5.5 1.5 + - - +
247A TYR* 3.6 51.7 + - + -
401A NAD 2.9 34.7 + - - +
31B GLN* 5.2 8.1 + - - +
247B TYR* 5.4 2.9 + - - -
248B PHE* 6.0 0.3 - - - -
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 1.3 76.2 - - - +
33A GLY* 1.3 67.1 + - - +
35A ASN* 3.2 4.9 + - - +
36A ILE* 3.0 39.8 + - + +
97A THR* 3.9 10.8 - - + -
138A ILE* 4.1 11.7 - - + -
246A ALA 3.9 2.7 - - - +
247A TYR* 3.6 29.2 - - + +
250A PRO* 4.0 6.3 - - + -
251A ALA* 4.0 16.4 - - - +
401A NAD 3.1 67.0 + - + +
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.6 11.9 - - - +
28A GLY 3.3 25.0 + - - -
29A SER* 4.3 0.2 - - - -
30A GLY 3.3 5.9 + - - -
32A ILE* 1.3 79.5 - - - +
34A GLY* 1.3 60.1 + - - +
36A ILE* 3.4 5.3 + - - +
37A ALA 3.3 15.9 + - - -
51A LEU* 3.5 16.6 - - - +
97A THR* 4.2 7.2 + - - +
401A NAD 4.3 0.4 + - - -
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER 4.3 1.8 - - - -
30A GLY 2.9 16.0 + - - -
31A GLN 4.2 0.4 - - - -
33A GLY* 1.3 72.3 - - - +
35A ASN* 1.3 60.3 + - - +
37A ALA* 3.3 5.4 + - - +
38A TYR* 3.0 26.9 + - - +
51A LEU* 4.5 7.0 - - - -
62A LYS* 4.2 20.6 - - - -
66A ILE* 3.7 7.7 - - - +
248B PHE* 3.9 11.4 - - - -
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Residues in contact with ASN 35 (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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31A GLN 3.5 6.7 + - - +
32A ILE 3.2 4.3 + - - +
34A GLY* 1.3 73.9 - - - +
36A ILE* 1.3 65.8 + - - +
38A TYR* 3.3 5.3 + - - +
39A ILE* 3.0 28.1 + - - +
247A TYR* 3.2 41.3 + - - -
248A PHE* 3.5 19.8 - - - +
251A ALA* 3.5 19.7 - - + -
35B ASN* 4.0 10.0 - - - +
38B TYR* 4.0 15.7 - - + -
248B PHE* 3.8 17.5 - - - -
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Residues in contact with ILE 36 (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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24A ILE* 5.2 0.2 - - + -
26A VAL* 3.9 19.7 - - + -
32A ILE* 3.0 35.5 + - + +
33A GLY* 3.6 8.1 - - - +
34A GLY 3.3 0.2 - - - -
35A ASN* 1.3 75.7 - - - +
37A ALA* 1.3 54.3 + - - +
39A ILE* 3.8 0.7 - - - +
40A VAL* 2.8 54.0 + - + +
95A ILE* 3.7 40.6 - - + -
97A THR* 4.1 7.2 - - + -
138A ILE* 4.0 0.9 - - + -
251A ALA* 3.6 23.1 - - + +
254A ALA* 3.9 10.3 - - + -
255A VAL* 4.1 9.2 - - + -
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 3.3 7.5 + - - +
34A GLY 3.6 8.1 - - - +
35A ASN 3.3 0.2 - - - -
36A ILE* 1.3 78.1 - - - +
38A TYR* 1.3 55.3 + - - +
40A VAL* 4.0 0.3 - - - +
41A GLY* 2.8 31.5 + - - -
49A VAL* 3.6 35.9 - - + +
51A LEU* 3.9 16.8 - - + -
66A ILE* 3.9 20.1 - - + +
78A VAL* 4.3 5.5 - - + +
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Residues in contact with TYR 38 (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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34A GLY 3.0 13.9 + - - +
35A ASN* 3.3 10.8 - - - +
37A ALA* 1.3 76.0 - - - +
39A ILE* 1.3 59.0 + - + +
41A GLY* 3.9 0.5 - - - -
42A LYS* 2.9 28.8 + - - +
66A ILE* 3.9 14.5 - - + +
69A SER* 4.0 7.6 - - - -
70A MET* 4.4 2.3 - - - +
73A PHE* 3.8 18.4 - + - -
35B ASN* 4.0 14.4 - - - -
38B TYR* 4.5 12.3 - + - -
39B ILE* 3.6 40.8 - - + +
248B PHE* 2.7 67.9 + + + -
251B ALA* 3.8 11.4 - - - +
252B ALA* 3.8 6.8 + - - +
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Residues in contact with ILE 39 (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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35A ASN 3.0 21.0 + - - +
36A ILE* 3.9 2.7 - - - +
38A TYR* 1.3 74.5 - - + +
40A VAL* 1.3 60.6 + - - +
42A LYS* 3.3 3.6 + - + +
43A ASP* 2.9 45.5 + - - +
252A ALA* 5.6 1.8 - - - +
255A VAL* 4.1 22.0 - - + -
38B TYR* 3.6 40.4 - - + +
39B ILE* 4.2 13.2 - - + -
42B LYS* 3.8 31.2 - - + -
73B PHE* 4.2 11.2 - - + -
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Residues in contact with VAL 40 (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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24A ILE* 4.1 27.1 - - + -
36A ILE* 2.8 35.1 + - + +
39A ILE* 1.3 72.4 - - - +
41A GLY* 1.3 61.6 + - - +
43A ASP* 3.5 0.8 + - - -
44A ASN* 3.1 17.5 + - - -
45A LEU* 3.1 16.5 + - + -
46A ALA 3.7 21.1 - - - +
49A VAL* 3.3 28.3 - - + -
76A SER* 4.0 0.7 + - - -
95A ILE* 5.7 0.4 - - + -
255A VAL* 3.8 24.9 - - + -
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Residues in contact with GLY 41 (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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37A ALA 2.8 17.9 + - - -
40A VAL* 1.3 76.0 - - - +
42A LYS* 1.3 61.6 + - - +
44A ASN 3.1 3.8 + - - -
49A VAL* 4.6 0.6 - - - +
70A MET* 3.5 24.0 - - - -
74A SER* 2.7 28.1 + - - -
76A SER* 3.8 11.4 - - - -
78A VAL* 4.8 4.3 - - - -
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Residues in contact with LYS 42 (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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38A TYR 2.9 19.3 + - - +
39A ILE* 3.3 7.2 + - + +
41A GLY* 1.3 77.1 - - - +
43A ASP* 1.3 62.0 + - - +
44A ASN* 3.4 0.9 + - - +
70A MET* 3.7 1.2 - - - +
73A PHE* 3.7 57.7 - - + +
74A SER* 4.2 7.1 - - - -
39B ILE* 3.8 24.5 - - + -
42B LYS* 3.9 25.1 - - + +
43B ASP* 2.8 37.2 + - - -
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Residues in contact with ASP 43 (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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39A ILE* 2.9 35.0 + - - +
40A VAL 4.1 3.4 - - - +
42A LYS* 1.3 74.7 + - - +
44A ASN* 1.3 69.4 + - - +
45A LEU* 3.4 11.9 + - + +
255A VAL* 4.2 5.0 - - - +
259A GLU* 4.1 15.9 - - - +
42B LYS* 2.8 32.8 + - - -
73B PHE* 5.7 0.2 - - - -
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Residues in contact with ASN 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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20A ARG* 5.8 0.2 + - - -
40A VAL 3.1 4.2 + - - -
41A GLY 3.1 5.5 + - - -
42A LYS 3.2 0.6 - - - +
43A ASP* 1.3 80.1 - - - +
45A LEU* 1.3 62.3 + - - +
46A ALA* 3.4 2.4 + - - -
73A GLY 5.6 0.8 + - - -
74A SER* 3.5 19.8 + - - +
75A THR* 4.1 17.6 + - - +
76A SER* 3.0 31.1 + - - -
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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