Contacts of the helix formed by residues 30 - 43 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLY 3.5 4.6 + - - -
29B SER* 1.3 74.1 - - - +
31B GLN* 1.3 66.2 + - - +
32B ILE 3.4 2.0 - - - -
33B GLY 4.0 1.6 - - - +
34B GLY* 3.1 13.7 + - - -
58B ILE* 5.5 0.9 - - - -
62B LYS* 2.9 22.4 + - - -
97B THR* 4.6 0.4 + - - -
401B NAD 3.4 33.1 + - - -
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Residues in contact with GLN 31 (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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31A GLN* 5.2 8.1 + - - +
247A TYR* 5.5 3.8 + - - -
30B GLY* 1.3 74.3 - - - +
32B ILE* 1.3 63.1 + - - +
34B GLY* 4.3 0.3 - - - -
35B ASN* 3.5 24.3 + - - -
62B LYS* 4.6 6.0 - - - +
244B THR* 4.7 18.8 - - - +
245B THR 5.5 1.3 - - - +
247B TYR* 3.5 50.0 + - + -
401B NAD 2.9 35.2 + - - +
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN* 1.3 73.3 - - - +
33B GLY* 1.3 67.1 + - - +
35B ASN* 3.2 4.2 + - - +
36B ILE* 3.0 39.9 + - + +
97B THR* 3.9 10.5 - - + -
138B ILE* 4.0 14.6 - - + -
246B ALA 4.1 1.6 - - - +
247B TYR* 3.7 28.3 - - + +
250B PRO* 3.8 11.9 - - + -
251B ALA* 3.9 16.6 - - - +
401B NAD 3.1 60.9 + - + +
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 3.5 14.2 - - - +
28B GLY 3.4 23.3 - - - -
29B SER* 4.3 0.2 - - - -
30B GLY 3.5 5.6 + - - -
31B GLN 3.5 0.6 - - - -
32B ILE* 1.3 78.2 - - - +
34B GLY* 1.3 60.8 + - - +
36B ILE* 3.2 6.0 + - - +
37B ALA 3.1 18.0 + - - -
51B LEU* 3.7 13.8 - - - +
97B THR* 4.0 8.7 + - - +
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Residues in contact with GLY 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PHE* 4.0 17.9 - - - -
29B SER 4.4 2.4 - - - -
30B GLY 3.1 16.3 + - - -
31B GLN 4.3 0.7 - - - -
33B GLY* 1.3 74.2 - - - +
35B ASN* 1.3 55.9 + - - +
37B ALA* 3.3 2.6 + - - -
38B TYR* 3.0 28.1 + - - +
51B LEU* 4.4 7.6 - - - +
62B LYS* 4.3 13.2 - - - -
66B ILE* 3.5 9.1 - - - +
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Residues in contact with ASN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASN* 4.0 14.2 - - - +
38A TYR* 4.0 18.1 - - + +
248A PHE* 4.1 9.6 - - - -
31B GLN 3.5 6.8 + - - +
32B ILE 3.2 4.6 + - - +
34B GLY* 1.3 72.1 - - - +
36B ILE* 1.3 66.6 + - - +
38B TYR* 3.3 5.0 + - - +
39B ILE* 3.0 28.8 + - - +
247B TYR* 3.1 45.8 + - - -
248B PHE* 3.5 16.3 - - - +
251B ALA* 3.3 19.3 - - + -
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 5.2 0.7 - - + -
26B VAL* 3.8 21.8 - - + -
32B ILE* 3.0 33.9 + - + +
33B GLY 3.2 6.9 + - - +
35B ASN* 1.3 76.9 - - - +
37B ALA* 1.3 57.9 + - - +
39B ILE* 3.8 0.5 - - - +
40B VAL* 2.8 48.8 + - + +
95B ILE* 3.7 40.6 - - + -
97B THR* 4.2 7.2 - - + -
138B ILE* 4.0 0.7 - - + -
251B ALA* 3.7 22.2 - - - +
254B ALA* 4.0 9.9 - - + -
255B VAL* 4.3 8.5 - - + -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 4.8 0.2 - - - +
33B GLY 3.1 3.8 + - - -
34B GLY 3.3 8.0 + - - +
36B ILE* 1.3 77.7 - - - +
38B TYR* 1.3 57.2 + - - +
40B VAL* 3.9 0.5 - - - +
41B GLY* 2.9 27.9 + - - -
49B VAL* 3.8 30.3 - - + +
51B LEU* 3.8 28.0 - - + -
66B ILE* 3.7 19.7 - - + +
78B VAL* 4.2 4.9 - - + +
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Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASN* 4.0 15.5 - - + -
38A TYR* 4.5 11.7 - + - -
39A ILE* 3.6 38.8 - - + +
248A PHE* 2.7 66.6 + + + -
251A ALA* 3.9 5.5 - - - +
252A ALA* 3.8 11.4 + - - +
34B GLY 3.0 13.3 + - - +
35B ASN* 3.3 10.8 - - - +
37B ALA* 1.3 77.7 - - - +
39B ILE* 1.3 59.7 + - + +
41B GLY* 3.8 0.9 - - - -
42B LYS* 2.9 28.8 + - - +
66B ILE* 3.8 12.5 - - + +
69B SER* 3.9 9.9 - - - -
70B MET* 4.3 2.3 - - - +
73B PHE* 3.9 17.5 - + - -
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Residues in contact with ILE 39 (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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38A TYR* 3.6 41.1 - - + +
39A ILE* 4.2 13.5 - - + -
42A LYS* 3.8 30.5 - - + -
73A PHE* 4.3 12.6 - - + -
35B ASN 3.0 19.6 + - - +
36B ILE 4.0 1.6 - - - +
38B TYR* 1.3 76.9 - - + +
40B VAL* 1.3 66.5 + - - +
42B LYS* 3.4 3.8 + - + +
43B ASP* 3.0 38.8 + - - +
251B ALA* 5.6 0.2 - - + -
252B ALA* 5.6 0.9 - - - -
255B VAL* 4.1 23.3 - - + -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.0 26.2 - - + -
36B ILE* 2.8 32.3 + - + +
37B ALA 3.9 2.5 - - - +
39B ILE* 1.3 76.3 - - - +
41B GLY* 1.3 62.2 + - - +
43B ASP* 3.4 1.4 + - - -
44B ASN* 3.0 17.3 + - - -
45B LEU* 3.1 25.3 + - + -
46B ALA* 3.8 22.0 - - + +
49B VAL* 3.5 26.0 - - + -
76B SER* 4.2 0.2 + - - -
95B ILE* 5.8 0.7 - - + -
255B VAL* 3.9 20.2 - - + -
258B ALA* 5.9 0.2 - - + -
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Residues in contact with GLY 41 (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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37B ALA 2.9 17.5 + - - -
38B TYR 3.8 0.7 - - - -
40B VAL* 1.3 76.4 - - - +
42B LYS* 1.3 62.2 + - - +
44B ASN* 2.9 5.0 + - - -
46B ALA 4.8 0.2 - - - -
49B VAL* 4.8 0.4 - - - +
70B MET* 3.5 23.8 - - - -
74B SER* 2.7 27.2 + - - -
76B SER* 3.9 11.7 - - - -
78B VAL* 4.9 4.3 - - - -
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Residues in contact with LYS 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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39A ILE* 3.8 23.8 - - + -
42A LYS* 3.9 28.5 - - + +
43A ASP* 2.8 33.3 + - - -
38B TYR 2.9 17.7 + - - +
39B ILE* 3.4 7.8 + - + +
41B GLY* 1.3 75.0 - - - +
43B ASP* 1.3 63.1 + - - +
44B ASN* 3.2 0.7 + - - +
70B MET* 3.8 1.4 - - - +
73B PHE* 3.7 65.5 - - + +
74B SER* 4.3 4.2 - - - -
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Residues in contact with ASP 43 (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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42A LYS* 2.8 32.9 + - - -
73A PHE* 5.8 0.2 - - - -
39B ILE* 3.0 32.7 + - - +
40B VAL* 4.0 3.8 - - - +
42B LYS* 1.3 79.0 + - - +
44B ASN* 1.3 69.1 + - - +
45B LEU* 3.2 11.8 + - + +
255B VAL* 4.4 3.5 - - - +
259B GLU* 4.1 15.6 - - - +
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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