Contacts of the strand formed by residues 17 - 26 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15I PRO* 3.6 0.9 - - - +
16I ASN* 1.3 99.9 - - - +
18I VAL* 1.3 61.9 + - - +
19I SER* 5.0 1.0 + - - -
59J ALA* 4.2 2.9 - - - +
60J GLU 3.2 11.2 - - - +
62J VAL* 3.7 21.7 - - + +
65J PRO* 4.7 2.6 - - - +
161J ALA 5.2 0.2 + - - -
162J LEU* 3.3 12.3 - - - +
163J TRP* 3.0 45.6 + - - +
164J TYR 3.6 2.2 + - - -
165J LYS* 3.5 32.1 - - + +
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Residues in contact with VAL 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I THR* 1.3 76.0 - - - +
19I SER* 1.3 67.2 + - - +
20I LEU* 4.6 1.3 - - + -
55J MET* 3.6 22.9 - - + -
60J GLU 3.0 4.4 + - - +
61J ILE* 3.3 36.4 - - + +
62J VAL 2.9 23.2 + - - +
95J VAL* 4.6 9.2 - - + -
107J ILE* 4.5 7.9 - - + -
160J ALA* 4.0 25.4 - - + -
161J ALA 3.3 5.8 - - - +
162J LEU* 3.8 19.7 - - + -
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Residues in contact with SER 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I THR* 5.0 1.0 + - - -
18I VAL* 1.3 74.3 - - - +
20I LEU* 1.3 66.0 + - - +
21I VAL* 3.8 1.8 + - - +
61J ILE* 5.3 0.2 - - - -
62J VAL* 2.8 27.2 + - - +
63J PRO 3.5 9.5 + - - -
64J LEU* 3.8 30.5 - - - -
65J PRO* 3.5 11.4 - - - +
159J ALA 3.6 0.9 - - - +
160J ALA* 3.3 2.1 - - - -
161J ALA* 2.8 40.5 + - - +
163J TRP* 6.0 0.2 - - - +
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Residues in contact with LEU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I VAL* 4.6 3.1 - - + -
19I SER* 1.3 73.6 - - - +
21I VAL* 1.3 66.4 + - - +
61J ILE* 5.1 12.3 - - + +
62J VAL 4.7 1.0 + - - -
64J LEU 5.8 0.7 + - - -
93J ILE* 3.6 20.0 - - + +
95J VAL* 3.6 25.1 - - + -
142J GLU* 4.0 16.2 - - + +
143J SER* 3.8 40.8 - - - +
144J ILE* 3.8 22.8 - - + +
159J ALA 3.3 1.1 - - - -
160J ALA* 3.7 11.2 - - + -
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Residues in contact with VAL 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I SER 4.6 3.4 - - - +
20I LEU* 1.3 81.1 - - - +
22I ALA* 1.3 64.3 + - - +
41I ALA* 3.5 31.9 - - + +
43I ILE* 4.6 18.4 - - + -
64J LEU* 4.0 34.5 - - + -
144J ILE* 3.8 9.5 - - - +
157J PHE* 4.7 0.9 - - + -
158J ALA* 3.4 0.3 - - - -
159J ALA* 2.8 52.7 + - + +
161J ALA* 5.5 1.6 - - + -
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Residues in contact with ALA 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL* 1.3 81.2 - - - +
23I GLY* 1.3 59.2 + - - +
40I ASN* 4.3 2.8 - - - +
41I ALA* 3.4 17.7 - - - -
144J ILE* 3.9 22.8 - - + +
145J ALA 4.4 2.7 - - - +
146J VAL* 3.9 20.6 - - + -
157J PHE* 3.2 13.7 - - - +
158J ALA* 4.1 7.4 - - + -
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Residues in contact with GLY 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I ALA* 1.3 76.0 - - - +
24I SER* 1.3 60.3 + - - -
37I ALA* 3.8 16.4 + - - -
40I ASN* 3.2 14.8 - - - -
41I ALA* 3.8 3.5 - - - +
146J VAL* 3.6 11.9 - - - +
157J PHE* 2.8 35.2 + - - +
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Residues in contact with SER 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I GLY* 1.3 74.6 - - - -
25I SER* 1.3 67.8 + - - +
37I ALA* 4.0 4.5 - - - -
40I ASN* 3.1 22.9 + - - +
146J VAL* 4.3 10.9 - - - +
147J GLU 4.2 4.7 + - - -
148J HIS* 3.0 33.2 + - - +
155J CYS 3.0 15.7 - - - -
156J ALA* 4.2 3.1 - - - -
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Residues in contact with SER 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I SER* 1.3 79.4 + - - +
26I GLU* 1.3 81.1 + - - +
33I ALA* 3.9 5.5 - - - +
36I GLY* 3.3 36.2 - - - -
37I ALA* 3.4 2.0 - - - +
40I ASN* 5.2 0.2 - - - -
148J HIS* 3.9 10.2 + - - -
154J GLY* 3.3 1.4 - - - -
155J CYS* 2.9 31.4 + - - +
133L MET* 4.1 4.5 - - - +
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Residues in contact with GLU 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I SER* 1.3 89.8 + - - +
27I GLY* 1.3 59.3 + - - +
33I ALA* 3.8 6.1 - - - -
148J HIS* 2.8 27.9 + - + +
150J VAL* 3.6 2.4 - - - -
151J GLU* 2.9 47.3 + - - +
152J LYS* 2.9 25.5 + - - +
153J LEU 3.1 20.9 + - - +
154J GLY* 3.7 1.2 - - - -
133L MET* 3.9 8.7 - - - +
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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