Contacts of the helix formed by residues 29 - 42 (chain K) in PDB entry 1N13
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 THR 29 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122H THR* 5.6 4.7 - - + -
126H MET* 3.8 27.1 - - + +
129H ILE* 5.2 2.7 - - + -
27K GLY 3.9 0.2 - - - -
28K GLU* 1.3 85.7 - - + +
30K PRO* 1.3 76.7 - - - +
31K LEU 3.6 2.6 + - - -
32K ASN* 2.6 37.4 + - - +
33K ALA* 2.9 23.0 + - - +
153L LEU* 3.8 6.6 - - - +
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Residues in contact with PRO 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K THR* 1.3 87.1 - - - +
31K LEU* 1.3 57.1 + - - +
33K ALA* 3.2 3.5 + - - +
34K PHE* 2.9 28.6 + - - +
81L ILE* 3.6 30.5 - - + +
153L LEU* 3.9 23.8 - - + -
7002L MRD 4.1 8.1 - - + +
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H MET* 3.6 16.1 - - - +
109H GLU* 3.3 39.0 - - + +
126H MET* 3.6 15.5 - - + +
7012H AG2 3.6 41.0 - - + +
29K THR* 3.2 1.2 + - - -
30K PRO* 1.3 79.2 - - - +
32K ASN* 1.3 58.9 + - - +
34K PHE* 3.4 3.2 + - + +
35K ASP* 2.9 27.5 + - - +
7002L MRD 3.7 43.6 - - + +
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Residues in contact with ASN 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H MET* 3.7 14.1 - - - +
126H MET* 3.0 42.5 + - - +
129H ILE* 3.6 27.3 - - + +
130H GLY* 3.9 5.1 - - - +
133H MET* 3.7 13.5 - - - +
27K GLY* 4.3 2.0 - - - -
28K GLU 4.2 7.4 - - - +
29K THR* 2.6 38.7 + - - +
31K LEU* 1.3 73.9 - - - +
33K ALA* 1.3 61.0 + - - +
35K ASP* 3.4 5.7 + - - +
36K GLY 2.9 23.2 + - - -
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Residues in contact with ALA 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K SER* 3.9 9.0 - - - +
26K GLU 3.9 4.0 - - - -
27K GLY* 3.8 18.5 - - - +
29K THR 2.9 13.4 + - - +
30K PRO 3.5 8.3 - - - +
32K ASN* 1.3 74.1 - - - +
34K PHE* 1.3 58.4 + - - +
36K GLY* 3.2 1.6 + - - -
37K ALA* 2.9 28.6 + - - +
81L ILE* 5.0 0.4 - - + -
153L LEU* 3.5 22.2 - - + +
155L CYS* 3.7 18.4 - - + +
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Residues in contact with PHE 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G SER* 3.4 24.0 - - - -
7012H AG2 3.8 15.5 - - + -
30K PRO 2.9 17.0 + - - +
31K LEU* 3.5 4.9 - - + +
33K ALA* 1.3 73.4 - - - +
35K ASP* 1.3 66.2 + - - +
37K ALA* 3.0 4.2 + - - +
38K LEU* 3.0 46.1 + - + +
48K LEU* 4.8 1.3 - - + -
77L TYR* 4.1 14.4 - + - -
79L TYR* 3.8 38.1 - + - -
81L ILE* 4.5 0.4 - - + -
155L CYS* 3.8 15.8 - - - +
157L PHE* 4.0 14.6 - + - -
7002L MRD 3.7 39.0 - - + -
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Residues in contact with ASP 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H LEU* 4.0 4.1 - - - +
108H MET* 3.9 20.3 - - + +
130H GLY* 4.0 5.5 - - - -
133H MET* 5.1 2.8 - - + +
134H ARG* 2.8 45.7 + - - -
7012H AG2 3.0 31.8 + - - -
31K LEU 2.9 17.0 + - - +
32K ASN* 3.5 6.7 - - - +
34K PHE* 1.3 76.4 - - - +
36K GLY* 1.3 61.7 + - - +
38K LEU* 3.2 4.2 + - - +
39K LEU* 3.0 26.1 + - - +
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Residues in contact with GLY 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H MET* 3.5 25.3 - - - +
25K SER* 3.3 14.7 - - - -
32K ASN 2.9 11.1 + - - -
33K ALA 3.6 3.6 - - - -
34K PHE 3.2 0.2 - - - -
35K ASP* 1.3 77.6 - - - +
37K ALA* 1.3 55.1 + - - +
39K LEU* 3.3 9.0 + - - +
40K ASN* 2.9 28.6 + - - +
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Residues in contact with ALA 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K GLY* 3.7 15.5 - - - +
24K SER* 3.9 5.8 - - - -
25K SER* 3.4 6.0 - - - -
33K ALA 2.9 12.9 + - - +
34K PHE 3.0 8.3 + - - +
36K GLY* 1.3 74.0 - - - +
38K LEU* 1.3 60.7 + - - +
40K ASN* 3.3 3.3 + - - +
41K ALA* 3.0 27.9 + - - +
155L CYS* 3.8 34.1 - - - +
157L PHE* 3.9 8.7 - - + -
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Residues in contact with LEU 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G SER 4.2 0.2 - - - +
7012H AG2 3.4 37.7 - - - +
34K PHE* 3.0 37.4 + - + +
35K ASP 3.6 6.1 - - - +
37K ALA* 1.3 73.6 - - - +
39K LEU* 1.3 61.5 + - - +
41K ALA* 3.2 6.6 + - - +
42K GLY 3.0 8.8 + - - -
43K ILE* 2.9 35.1 + - + +
44K GLY* 3.6 11.4 - - - -
48K LEU* 3.8 20.0 - - + -
157L PHE* 3.5 42.8 - - + -
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Residues in contact with LEU 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H MET* 4.7 16.2 - - + +
134H ARG* 3.7 51.6 - - + +
35K ASP* 3.0 23.3 + - - +
36K GLY* 3.6 11.4 - - - +
37K ALA 3.3 0.2 - - - -
38K LEU* 1.3 77.2 - - - +
40K ASN* 1.3 60.9 + - - +
42K GLY* 3.1 13.2 + - - -
44K GLY* 3.7 23.3 - - - +
45K ASN* 4.2 8.5 - - - +
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Residues in contact with ASN 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K ALA 4.4 1.9 - - - +
23K GLY* 3.2 8.3 - - - -
24K SER* 2.9 41.7 + - - +
25K SER* 5.0 0.4 - - - -
36K GLY 2.9 14.8 + - - +
37K ALA 3.5 5.2 - - - +
38K LEU 3.2 0.2 - - - -
39K LEU* 1.3 76.4 - - - +
41K ALA* 1.3 60.4 - - - +
42K GLY* 3.6 0.5 + - - -
146L VAL* 5.5 0.9 - - - +
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Residues in contact with ALA 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K VAL* 3.7 24.2 - - + +
22K ALA* 3.4 36.2 + - - +
23K GLY* 3.7 0.9 - - - +
37K ALA 3.0 16.5 + - - +
38K LEU 3.5 6.1 - - - +
39K LEU 3.2 0.4 - - - -
40K ASN* 1.3 78.8 - - - +
42K GLY* 1.3 56.5 + - - +
43K ILE* 3.6 2.0 - - + -
64L LEU* 4.7 1.6 - - - +
157L PHE* 4.1 16.6 - - + -
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Residues in contact with GLY 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K LEU 3.0 2.8 + - - -
39K LEU 3.1 12.6 + - - -
40K ASN 3.3 0.6 + - - -
41K ALA* 1.3 78.7 - - - +
43K ILE* 1.3 61.4 + - - +
44K GLY 3.6 3.1 + - - -
64L LEU* 3.5 19.8 - - - +
67L LEU* 5.8 0.7 - - - +
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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