Contacts of the strand formed by residues 17 - 26 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PRO* 3.6 0.9 - - - +
16A ASN* 1.3 96.5 + - - +
18A VAL* 1.3 67.6 + - - +
19A SER* 5.1 0.7 + - - -
59B ALA* 4.3 0.2 - - - +
60B GLU 3.3 5.4 - - - +
62B VAL* 3.7 20.4 - - + -
65B PRO* 4.4 8.5 - - + +
161B ALA 4.3 0.4 + - - -
162B LEU* 3.3 6.8 - - - +
163B TRP* 3.0 48.0 + - - +
164B TYR 3.6 0.7 + - - -
165B LYS* 3.6 37.7 - - + +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A THR* 1.3 79.7 - - - +
19A SER* 1.3 66.3 + - - +
20A LEU* 4.5 9.0 - - + -
55B MET* 3.5 41.7 - - + -
56B PRO* 4.8 0.7 - - + -
59B ALA* 4.6 4.9 - - + -
60B GLU 2.9 7.5 + - - +
61B ILE* 3.2 11.6 - - + +
62B VAL 2.9 23.6 + - - +
95B VAL* 4.6 10.8 - - + -
107B ILE* 4.6 2.9 - - + -
160B ALA* 4.1 24.5 - - + -
161B ALA 3.4 5.2 - - - +
162B LEU* 4.1 19.3 - - + -
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A THR* 5.1 1.2 + - - -
18A VAL* 1.3 75.9 - - - +
20A LEU* 1.3 65.1 + - - +
21A VAL* 3.8 2.5 + - - +
61B ILE* 5.4 0.2 - - - -
62B VAL* 2.8 26.2 + - - +
63B PRO 3.5 0.7 + - - -
64B LEU* 3.4 41.3 - - - -
65B PRO* 3.5 10.6 - - - +
159B ALA 3.6 0.9 - - - +
160B ALA* 3.3 2.1 - - - -
161B ALA* 2.8 39.6 + - - +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.5 3.6 - - + -
19A SER* 1.3 73.1 - - - +
21A VAL* 1.3 65.8 + - - +
61B ILE* 5.0 14.6 - - + +
62B VAL 4.7 1.0 + - - -
64B LEU 5.9 0.5 + - - -
93B ILE* 3.8 15.7 - - + +
95B VAL* 3.8 14.8 - - + -
142B GLU* 4.1 14.8 - - + +
143B SER* 3.9 39.0 - - - +
144B ILE* 3.8 23.0 - - + +
159B ALA 3.3 1.3 - - - -
160B ALA* 3.7 26.9 - - + -
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER* 4.5 5.8 - - - +
20A LEU* 1.3 80.8 - - - +
22A ALA* 1.3 64.1 + - - +
41A ALA* 3.5 27.4 - - + +
43A ILE* 3.9 29.8 - - + -
64B LEU* 4.1 34.3 - - + -
144B ILE* 3.8 8.9 - - - +
157B PHE* 4.6 0.4 - - + -
158B ALA* 3.5 0.3 - - - -
159B ALA* 2.8 44.3 + - + +
161B ALA* 5.4 2.5 - - + -
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 1.3 79.3 - - - +
23A GLY* 1.3 58.8 + - - +
40A ASN* 4.3 2.8 - - - +
41A ALA* 3.4 18.3 - - - +
144B ILE* 3.8 23.9 - - + +
145B ALA 4.5 2.7 - - - +
146B VAL* 3.8 20.9 - - + -
157B PHE* 3.2 13.9 - - - +
158B ALA* 4.1 7.4 - - + -
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 1.3 75.5 - - - +
24A SER* 1.3 61.4 + - - -
37A ALA* 3.8 17.2 + - - -
40A ASN* 3.3 14.1 - - - -
41A ALA* 3.8 3.2 - - - +
146B VAL* 3.7 11.5 - - - +
157B PHE* 2.9 35.0 + - - +
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Residues in contact with SER 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLY* 1.3 76.3 - - - -
25A SER* 1.3 66.3 + - - +
37A ALA* 3.9 4.5 - - - -
40A ASN* 3.0 23.8 + - - +
146B VAL* 4.4 11.2 - - - +
147B GLU 4.2 5.1 + - - -
148B HIS* 3.1 32.7 + - - +
155B CYS 3.1 15.0 - - - -
156B ALA* 4.2 3.1 - - - -
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A SER* 1.3 79.8 + - - +
26A GLU* 1.3 75.0 + - - +
33A ALA* 3.9 5.5 - - - +
36A GLY* 3.3 35.5 - - - -
37A ALA* 3.4 2.0 - - - +
40A ASN* 5.1 0.2 - - - -
148B HIS* 4.0 10.6 + - - -
154B GLY* 3.3 0.9 - - - -
155B CYS* 2.9 31.2 + - - +
133F MET* 4.1 5.0 - - - +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 1.3 91.2 + - - +
27A GLY* 1.3 57.9 + - - +
33A ALA* 3.8 6.1 - - - -
148B HIS* 2.8 30.3 + - + +
150B VAL* 3.6 2.6 - - - -
151B GLU* 2.9 44.9 + - - +
152B LYS* 2.9 25.1 + - - +
153B LEU 3.0 22.5 + - - +
133F MET* 4.0 8.1 - - - +
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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