Contacts of the strand formed by residues 17 - 26 (chain C) 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 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C PRO* 3.7 0.9 - - - +
16C ASN* 1.3 95.6 + - - +
18C VAL* 1.3 67.9 + - - +
19C SER* 5.0 1.4 + - - -
56D PRO* 6.0 0.5 - - - +
59D ALA* 4.2 0.2 - - - +
60D GLU* 3.2 8.7 - - + +
62D VAL* 3.6 33.5 - - + +
65D PRO* 5.2 2.9 - - - +
161D ALA 5.2 0.2 + - - -
162D LEU* 3.3 6.8 - - - +
163D TRP* 2.9 44.1 + - - +
164D TYR 3.6 3.5 + - - -
165D LYS* 3.7 24.0 - - + +
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR* 1.3 81.0 - - - +
19C SER* 1.3 67.8 + - - +
20C LEU* 4.5 6.7 - - + -
55D MET* 3.5 42.2 - - + -
56D PRO* 4.9 1.3 - - + -
59D ALA* 4.9 1.8 - - + -
60D GLU 2.9 8.0 + - - +
61D ILE* 3.2 13.9 - - + +
62D VAL 2.9 24.1 + - - -
95D VAL* 5.3 3.1 - - + -
107D ILE* 4.4 8.5 - - + -
160D ALA* 4.0 25.8 - - + -
161D ALA 3.3 6.1 - - - +
162D LEU* 4.1 17.7 - - + -
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Residues in contact with SER 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR* 5.0 1.2 + - - -
18C VAL* 1.3 75.4 - - - +
20C LEU* 1.3 64.9 + - - +
21C VAL* 3.8 3.1 + - - +
61D ILE* 5.2 0.4 - - - -
62D VAL* 2.8 25.0 + - - +
63D PRO 3.4 10.4 + - - -
64D LEU* 3.5 34.1 - - - -
65D PRO* 3.6 8.5 - - - +
159D ALA 3.6 0.5 - - - +
160D ALA* 3.3 2.6 - - - -
161D ALA* 2.8 36.1 + - - +
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C VAL* 4.5 7.2 - - + -
19C SER* 1.3 72.3 - - - +
21C VAL* 1.3 63.8 + - - +
61D ILE* 4.9 11.0 - - + +
62D VAL 4.7 1.0 + - - -
93D ILE* 4.0 16.6 - - + +
94D SER* 4.9 0.4 - - - -
95D VAL* 4.0 18.8 - - + -
142D GLU* 3.7 38.4 - - + +
143D SER* 4.0 13.2 - - - +
144D ILE* 3.3 26.6 - - + +
159D ALA 3.4 0.9 - - - -
160D ALA* 3.6 29.4 - - + -
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER 4.6 3.6 - - - +
20C LEU* 1.3 79.7 - - - +
22C ALA* 1.3 64.2 + - - +
41C ALA* 3.6 26.7 - - + +
43C ILE* 3.8 31.2 - - + -
64D LEU* 4.0 36.3 - - + -
144D ILE* 3.2 7.8 - - - +
157D PHE* 4.6 0.4 - - + -
158D ALA* 3.4 0.2 - - - -
159D ALA* 2.8 44.2 + - + +
161D ALA* 5.5 2.5 - - + -
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 1.3 79.5 - - - +
23C GLY* 1.3 59.7 + - - +
40C ASN* 4.1 3.1 - - - +
41C ALA* 3.4 18.3 + - - +
144D ILE* 3.7 16.9 - - + +
145D ALA 4.5 7.4 - - - +
146D VAL* 4.0 18.2 - - + -
157D PHE* 3.2 13.7 - - - +
158D ALA* 4.0 8.7 - - + +
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ALA* 1.3 76.4 - - - +
24C SER* 1.3 62.6 + - - -
37C ALA 3.8 16.2 - - - -
40C ASN* 3.2 14.1 - - - -
41C ALA* 3.7 4.3 - - - +
146D VAL* 3.6 10.8 - - - +
157D PHE* 2.8 34.9 + - - +
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Residues in contact with SER 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLY* 1.3 74.9 - - - -
25C SER* 1.3 66.9 + - - +
37C ALA* 3.9 4.7 - - - -
40C ASN* 3.0 26.9 + - - +
146D VAL* 4.2 11.6 - - - +
147D GLU 3.9 5.9 + - - -
148D HIS* 3.1 32.3 + - - +
155D CYS 3.1 15.3 - - - -
156D ALA* 4.2 3.8 - - - -
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Residues in contact with SER 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B MET* 3.9 5.5 - - - +
24C SER* 1.3 78.6 - - - +
26C GLU* 1.3 80.1 + - - +
33C ALA* 3.9 5.2 - - - +
36C GLY* 3.3 36.8 - - - -
37C ALA* 3.4 2.6 - - - +
40C ASN* 5.0 0.4 - - - -
148D HIS* 3.8 11.5 + - - -
154D GLY* 3.3 1.4 - - - -
155D CYS* 2.9 31.4 + - - +
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B MET* 3.9 8.7 - - - +
25C SER* 1.3 91.4 + - - +
27C GLY* 1.3 58.2 + - - +
33C ALA* 3.8 6.5 - - - -
148D HIS* 2.8 29.4 + - + +
150D VAL* 3.6 2.8 - - - -
151D GLU* 2.9 46.9 + - + +
152D LYS* 3.0 24.8 + - - +
153D LEU 3.0 20.6 + - - +
154D GLY* 3.8 1.0 - - - -
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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
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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