Contacts of the strand formed by residues 17 - 26 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15G PRO* 3.6 0.9 - - - +
16G ASN* 1.3 98.1 + - - +
18G VAL* 1.3 65.8 + - - +
19G SER* 5.2 0.5 + - - -
56H PRO* 6.1 0.2 - - - +
59H ALA* 4.2 0.4 - - - +
60H GLU* 3.2 8.3 - - + +
62H VAL* 3.6 29.1 - - + +
65H PRO* 4.5 5.3 - - + +
161H ALA 4.3 0.6 + - - -
162H LEU* 3.3 7.6 - - - +
163H TRP* 3.0 49.2 + - - +
164H TYR 3.6 1.4 + - - -
165H LYS* 3.5 26.0 - - + +
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Residues in contact with VAL 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G THR* 1.3 78.2 - - - +
19G SER* 1.3 65.3 + - - +
20G LEU* 4.4 6.3 - - + -
55H MET* 3.5 33.2 - - + -
56H PRO* 5.1 0.9 - - + -
59H ALA* 4.6 3.4 - - + -
60H GLU 2.9 6.6 + - - +
61H ILE* 3.2 28.3 - - + +
62H VAL* 2.9 24.0 + - - -
95H VAL* 4.5 5.6 - - + -
107H ILE* 4.6 2.7 - - + -
160H ALA* 4.1 24.5 - - + -
161H ALA 3.4 3.8 - - - +
162H LEU* 3.4 24.7 - - + -
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Residues in contact with SER 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G THR* 5.2 1.2 + - - -
18G VAL* 1.3 75.7 - - - +
20G LEU* 1.3 65.3 + - - +
21G VAL* 3.8 3.5 + - - +
61H ILE* 5.3 0.2 - - - -
62H VAL* 2.9 25.2 + - - +
63H PRO 3.4 11.1 + - - -
64H LEU* 3.8 30.3 - - - -
65H PRO* 3.5 12.2 - - - +
159H ALA 3.6 0.5 - - - +
160H ALA* 3.3 2.1 - - - -
161H ALA* 2.8 40.2 + - - +
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 4.4 21.9 + - + +
139B ASP* 3.9 10.6 - - - +
18G VAL* 4.4 3.4 - - + -
19G SER* 1.3 72.5 - - - +
21G VAL* 1.3 65.0 + - - +
61H ILE* 4.9 10.7 - - + +
62H VAL 4.7 1.0 + - - -
93H ILE* 3.9 14.8 - - + +
95H VAL* 3.6 27.1 - - + -
142H GLU* 3.7 35.4 - - + +
143H SER* 3.9 20.0 - - - +
144H ILE* 3.3 22.8 - - + +
159H ALA 3.4 1.6 - - - +
160H ALA* 3.7 21.1 - - + -
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Residues in contact with VAL 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASP* 4.3 15.7 - - - +
19G SER 4.6 4.7 - - - +
20G LEU* 1.3 80.8 - - - +
22G ALA* 1.3 64.4 + - - +
41G ALA* 3.5 26.5 - - + +
43G ILE* 3.7 31.4 - - + -
64H LEU* 4.3 30.5 - - + -
144H ILE* 3.3 8.0 - - - +
157H PHE* 4.6 0.4 - - + -
158H ALA* 3.5 0.2 - - - -
159H ALA* 2.8 43.7 + - + +
161H ALA* 5.4 3.1 - - + -
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Residues in contact with ALA 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LYS* 5.3 9.0 + - - -
139B ASP* 4.9 4.0 + - - +
140B ARG* 5.3 1.9 + - - -
21G VAL* 1.3 79.7 - - - +
23G GLY* 1.3 59.9 + - - +
40G ASN* 4.1 2.9 - - - +
41G ALA* 3.3 18.7 + - - +
144H ILE* 3.8 16.7 - - + +
145H ALA 4.4 7.6 - - - +
146H VAL* 3.9 19.6 - - + +
157H PHE* 3.1 13.9 - - - +
158H ALA* 4.1 8.3 - - + -
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Residues in contact with GLY 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G ALA* 1.3 76.6 - - - +
24G SER* 1.3 61.6 + - - -
37G ALA 3.7 16.6 - - - -
40G ASN* 3.2 13.2 - - - -
41G ALA* 3.7 5.0 - - - +
146H VAL* 3.7 10.9 - - - +
157H PHE* 2.8 34.9 + - - +
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Residues in contact with SER 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G GLY* 1.3 75.2 - - - -
25G SER* 1.3 67.2 + - - +
37G ALA* 3.9 4.3 - - - -
40G ASN* 2.9 27.7 + - - +
146H VAL* 4.2 11.9 - - - +
147H GLU 4.0 7.8 + - - -
148H HIS* 3.4 29.0 + - - -
155H CYS 3.1 15.0 - - - -
156H ALA* 4.3 2.9 - - - -
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Residues in contact with SER 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G SER* 1.3 78.2 + - - +
26G GLU* 1.3 78.9 + - - +
33G ALA* 3.9 5.3 - - - +
36G GLY* 3.3 36.6 - - - -
37G ALA* 3.4 2.6 - - - +
40G ASN* 5.0 0.2 - - - -
148H HIS* 3.8 11.5 + - - -
154H GLY* 3.3 0.9 - - - -
155H CYS* 2.8 32.7 + - - +
133J MET* 3.8 5.0 - - - +
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Residues in contact with GLU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G SER* 1.3 91.2 + - - +
27G GLY* 1.3 60.0 + - - +
33G ALA* 3.8 4.3 - - - -
148H HIS* 2.8 28.8 + - + +
150H VAL* 3.6 1.4 - - - -
151H GLU* 3.0 46.0 + - - +
152H LYS* 2.9 25.8 + - - +
153H LEU 3.0 26.0 + - - +
133J MET* 3.8 10.9 - - - +
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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