Contacts of the strand formed by residues 17 - 26 (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 17 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15K PRO* 3.6 0.9 - - - +
16K ASN* 1.3 83.7 + - - +
18K VAL* 1.3 61.7 + - - +
19K SER* 5.1 1.2 + - - -
56L PRO* 6.1 0.7 - - - +
59L ALA* 4.2 2.6 - - - +
60L GLU 3.2 6.3 - - - +
62L VAL* 3.7 31.4 - - + +
65L PRO* 5.2 2.8 - - - +
161L ALA 5.2 0.2 + - - -
162L LEU* 3.3 8.8 - - - +
163L TRP* 2.9 46.4 + - - +
164L TYR 3.6 1.9 + - - -
165L LYS* 3.3 41.7 - - + +
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Residues in contact with VAL 18 (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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17K THR* 1.3 76.8 - - - +
19K SER* 1.3 67.8 + - - +
20K LEU* 4.6 5.2 - - + -
55L MET* 3.6 27.6 - - + -
56L PRO* 6.4 0.2 - - + -
60L GLU 2.9 5.9 + - - -
61L ILE* 3.2 36.2 - - + +
62L VAL 2.9 23.4 + - - +
95L VAL* 4.8 3.1 - - + -
107L ILE* 4.4 8.5 - - + -
160L ALA* 3.9 26.7 - - + -
161L ALA 3.3 7.2 - - - +
162L LEU* 4.2 13.9 - - + -
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Residues in contact with SER 19 (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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17K THR* 5.1 1.0 + - - -
18K VAL* 1.3 75.6 - - - +
20K LEU* 1.3 65.8 + - - +
21K VAL* 3.8 3.3 + - - +
62L VAL* 2.8 26.1 + - - +
63L PRO 3.4 10.4 + - - -
64L LEU* 3.5 33.3 - - - -
65L PRO* 3.6 8.7 - - - +
159L ALA 3.6 1.0 - - - +
160L ALA* 3.3 2.1 - - - -
161L ALA* 2.8 41.1 + - - +
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Residues in contact with LEU 20 (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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18K VAL* 4.6 3.4 - - + -
19K SER* 1.3 72.9 - - - +
21K VAL* 1.3 65.1 + - - +
61L ILE* 4.9 13.6 - - + +
62L VAL 4.8 0.6 + - - -
64L LEU 6.0 0.2 + - - -
93L ILE* 3.9 15.3 - - + +
95L VAL* 3.7 20.4 - - + -
142L GLU* 3.7 37.9 - - + +
143L SER* 3.9 15.0 - - - +
144L ILE* 3.9 21.5 - - + +
159L ALA 3.3 2.0 - - - -
160L ALA* 3.7 27.6 - - + -
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Residues in contact with VAL 21 (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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19K SER* 4.6 5.6 - - - +
20K LEU* 1.3 79.5 - - - +
22K ALA* 1.3 63.8 + - - +
41K ALA* 3.7 23.8 - - + +
43K ILE* 3.8 33.0 - - + -
64L LEU* 4.0 35.0 - - + +
144L ILE* 4.0 8.2 - - - +
157L PHE* 4.5 0.6 - - + -
158L ALA* 3.4 0.5 - - - -
159L ALA* 2.8 45.8 + - + +
161L ALA* 5.3 2.9 - - + -
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Residues in contact with ALA 22 (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* 1.3 79.7 - - - +
23K GLY* 1.3 58.1 + - - +
40K ASN* 4.4 2.6 - - - +
41K ALA* 3.4 18.9 + - - +
144L ILE* 3.8 25.6 - - + +
145L ALA 4.5 2.2 - - - +
146L VAL* 3.9 20.1 - - + +
157L PHE* 3.2 14.6 - - - +
158L ALA* 4.0 8.5 - - + -
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Residues in contact with GLY 23 (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* 1.3 76.6 - - - +
24K SER* 1.3 60.5 + - - -
37K ALA* 3.7 17.5 + - - -
40K ASN* 3.2 13.9 - - - -
41K ALA* 3.7 5.7 - - - +
146L VAL* 3.6 10.3 - - - +
157L PHE* 2.9 34.4 + - - +
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Residues in contact with SER 24 (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* 1.3 75.5 - - - -
25K SER* 1.3 66.6 + - - +
37K ALA* 3.9 4.0 - - - -
40K ASN* 2.9 25.6 + - - +
146L VAL* 4.2 11.3 - - - +
147L GLU 4.0 5.4 + - - -
148L HIS* 3.1 32.0 + - - +
155L CYS 3.0 16.6 - - - -
156L ALA* 4.2 3.1 - - - -
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Residues in contact with SER 25 (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* 4.2 4.7 - - - +
24K SER* 1.3 78.3 - - - +
26K GLU* 1.3 79.2 + - - +
33K ALA* 3.9 5.2 - - - +
36K GLY* 3.3 36.0 + - - -
37K ALA* 3.4 2.6 - - - +
40K ASN* 5.0 0.4 - - - -
148L HIS* 3.9 11.5 + - - -
154L GLY* 3.2 1.2 - - - -
155L CYS* 2.8 31.4 + - - +
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Residues in contact with GLU 26 (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* 4.2 7.8 - - - +
25K SER* 1.3 90.8 + - - +
27K GLY* 1.3 58.3 + - - +
33K ALA* 3.9 5.3 - - - -
148L HIS* 2.8 29.8 + - + +
150L VAL* 3.5 3.6 - - - -
151L GLU* 2.9 46.5 + - + +
152L LYS* 2.9 25.8 + - - +
153L LEU 3.0 21.7 + - - +
154L GLY* 3.7 0.9 - - - -
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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