Contacts of the helix formed by residues 29 - 42 (chain X) in PDB entry 3NZ9
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 LEU 29 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27X TRP* 3.6 33.7 + - + +
28X LYS* 1.3 78.4 - - - +
30X LYS* 1.3 64.4 + - - +
31X LYS 3.2 1.8 - - - -
32X GLU* 3.0 20.1 + - + +
33X ILE* 2.9 31.2 + - - +
146X ILE* 4.2 12.3 - - + -
192X GLU* 3.4 38.4 - - + +
193X ASP* 4.7 0.9 - - + -
195X PHE* 4.2 17.7 - - + -
197X TYR* 3.8 33.4 - - + -
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Residues in contact with LYS 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X LYS 4.0 2.2 + - - -
29X LEU* 1.3 72.6 - - - +
31X LYS* 1.3 77.6 + - + +
33X ILE* 3.5 9.2 + - - +
34X SER* 2.9 27.2 + - - -
192X GLU* 3.3 8.4 + - - +
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Residues in contact with LYS 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29X LEU 3.2 1.0 - - - -
30X LYS* 1.3 94.5 - - + +
32X GLU* 1.3 60.4 + - - +
34X SER* 3.2 10.7 + - - -
35X TYR* 2.9 27.9 + - - +
190X ILE* 5.6 4.3 - - + -
192X GLU* 3.3 24.7 + - + +
197X TYR* 3.7 6.5 - - - +
199X PHE* 4.8 3.5 - - + -
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Residues in contact with GLU 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X ALA* 4.1 7.2 - - + +
27X TRP* 5.2 2.8 + - + -
29X LEU* 3.0 34.6 + - + +
31X LYS* 1.3 74.4 - - - +
33X ILE* 1.3 67.9 + - - +
35X TYR* 3.2 9.6 + - - +
36X PHE* 3.0 18.2 + - - +
144X THR* 2.7 45.2 + - + -
197X TYR* 3.4 19.4 + - + +
199X PHE* 4.0 5.0 - - + -
207X D2K 2.8 40.8 + - - -
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Residues in contact with ILE 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X LEU* 5.2 4.7 - - + -
28X LYS* 6.3 0.4 - - - -
29X LEU 2.9 22.0 + - - +
30X LYS* 3.8 10.5 - - + +
32X GLU* 1.3 79.0 - - + +
34X SER* 1.3 56.7 + - - +
36X PHE* 3.2 12.2 + - + +
37X LYS* 2.9 26.0 + - + +
207X D2K 3.1 88.2 - - + +
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Residues in contact with SER 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X LYS 2.9 15.3 + - - -
31X LYS* 3.2 18.8 + - - -
33X ILE* 1.3 75.9 - - - +
35X TYR* 1.3 56.9 + - - +
37X LYS* 3.8 9.6 - - - +
38X ARG* 2.9 29.8 + - - +
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Residues in contact with TYR 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X ILE* 4.5 12.1 - - + -
31X LYS 2.9 12.4 + - - +
32X GLU* 3.3 14.6 - - - +
34X SER* 1.3 73.4 - - - +
36X PHE* 1.3 60.1 + - - +
38X ARG* 3.1 24.1 + - - +
39X VAL* 2.7 60.0 + - + +
142X MET* 3.6 30.5 - - + +
143X ALA 5.9 0.9 - - - -
144X THR* 4.3 4.0 - - - -
177X LEU* 3.8 12.5 - - + +
185X VAL* 3.7 28.9 - - + -
199X PHE* 3.4 51.8 - + + +
200X GLU 4.9 2.1 + - - -
207X D2K 5.4 0.2 - - - -
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Residues in contact with PHE 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X ILE* 3.9 18.8 - - + -
32X GLU 3.0 9.1 + - - +
33X ILE* 3.4 15.3 - - + +
35X TYR* 1.3 76.9 - - - +
37X LYS* 1.3 63.1 + - + +
39X VAL* 3.8 0.3 - - - +
40X THR* 2.9 46.4 + - + +
55X VAL* 5.2 0.4 - - + -
72X LEU* 4.0 26.0 - - + -
75X ARG* 3.9 16.8 - - - -
123X ILE* 3.8 20.4 - - + -
207X D2K 3.3 88.4 - + + +
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Residues in contact with LYS 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X ILE 2.9 17.1 + - - +
34X SER* 3.8 9.2 - - - +
36X PHE* 1.3 78.4 - - + +
38X ARG* 1.3 65.2 + - - +
40X THR* 3.6 6.2 + - - -
41X SER* 2.7 33.2 + - - +
73X LYS* 6.0 3.4 - - - -
75X ARG* 3.9 25.8 - - - +
207X D2K 4.2 33.0 - - + +
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Residues in contact with ARG 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X SER* 2.9 19.6 + - - +
35X TYR* 3.7 27.4 - - - +
37X LYS* 1.3 77.6 - - - +
39X VAL* 1.3 65.3 + - - +
41X SER* 4.0 3.3 - - - -
42X PHE* 2.9 29.7 + - + +
181X VAL* 3.2 24.8 - - + +
183X THR* 3.0 38.0 + - - -
184X LYS 3.8 13.5 + - - -
185X VAL* 3.6 12.1 - - - +
186X PRO* 4.6 9.5 - - - +
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Residues in contact with VAL 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X ILE* 4.0 16.8 - - + -
35X TYR* 2.7 59.6 + - + +
38X ARG* 1.3 75.7 - - - +
40X THR* 1.3 62.7 + - - +
41X SER 3.2 1.2 + - - -
42X PHE* 3.7 12.9 + - - +
53X ASN* 4.3 1.0 + - - -
119X ARG* 5.4 2.4 + - - -
121X PHE* 3.5 31.2 - - + -
142X MET* 4.4 5.4 - - + -
180X TRP* 4.3 7.0 - - + -
181X VAL* 3.9 30.7 - - + +
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Residues in contact with THR 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X ILE* 3.9 20.0 - - + -
36X PHE* 2.9 47.3 + - + +
37X LYS 3.6 0.7 + - - -
39X VAL* 1.3 78.0 - - - +
41X SER* 1.3 56.8 + - - +
53X ASN* 3.0 26.5 + - - +
55X VAL* 4.0 11.6 - - + +
75X ARG* 2.9 42.5 + - - +
121X PHE* 3.9 20.8 - - + -
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Residues in contact with SER 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X LYS* 2.7 27.8 + - - +
38X ARG* 4.0 3.6 - - - -
40X THR* 1.3 76.2 - - - +
42X PHE* 1.3 64.3 + - - +
43X VAL* 3.3 10.9 + - - +
53X ASN* 3.4 7.5 + - - +
73X LYS 4.6 3.0 + - - -
74X GLY 5.6 3.6 - - - +
75X ARG* 3.6 28.7 + - - -
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Residues in contact with PHE 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38X ARG* 2.9 20.3 + - + +
39X VAL* 3.7 8.5 + - - +
41X SER* 1.3 73.8 - - - +
43X VAL* 1.3 70.8 + - - +
44X PRO* 3.7 32.5 - - + +
45X THR* 5.4 6.1 - - + -
53X ASN* 2.9 18.5 + - - -
118X ASN* 3.7 5.0 - - - +
119X ARG* 3.9 18.1 + - - -
179X SER 5.2 0.7 - - - -
180X TRP 4.0 6.7 - - - -
181X VAL* 3.2 28.7 - - - +
182X GLY* 3.5 28.7 - - - -
183X THR* 5.2 5.8 - - + -
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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
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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