Contacts of the strand formed by residues 26 - 31 (chain A) in PDB entry 1N9S
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 ARG 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ASN 4.2 0.6 + - - -
25A HIS* 1.3 69.8 - - - +
27A VAL* 1.3 54.4 + - - +
39A ARG* 5.0 5.9 + - - +
40A GLY* 3.5 25.0 - - - +
41A THR* 4.1 13.8 + - - +
54A ASN 5.5 0.2 + - - -
55A GLU* 4.8 12.1 + - - +
57A GLU* 4.6 13.9 + - - +
59A PHE* 6.0 0.6 - - - -
83A GLU* 3.4 8.9 - - - +
84A LEU* 2.5 63.0 + - + +
85A PRO 6.0 1.6 - - - -
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Residues in contact with VAL 27 (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 LEU* 4.1 26.7 - - + -
25A HIS* 3.2 17.5 - - + +
26A ARG* 1.3 76.7 - - - +
28A GLY* 1.3 62.7 + - - +
29A VAL* 4.4 3.8 - - + -
39A ARG* 3.5 0.5 - - - -
40A GLY 3.0 25.0 + - - +
42A LEU* 4.0 17.7 - - + -
53A LEU* 3.9 20.6 - - + -
81A ILE* 4.0 15.7 - - + -
82A ARG 3.1 15.5 - - - +
84A LEU* 3.2 20.0 - - - +
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Residues in contact with GLY 28 (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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27A VAL* 1.3 75.9 - - - +
29A VAL* 1.3 65.7 + - - -
30A LYS 3.7 1.0 + - - -
37A GLU* 4.0 10.9 - - - +
38A TYR 3.4 5.4 - - - -
39A ARG* 4.1 7.0 - - - -
80A TYR* 4.0 0.5 - - - +
81A ILE* 3.6 6.6 - - - +
82A ARG* 2.8 36.3 + - - +
84A LEU* 3.9 12.9 - - - +
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Residues in contact with VAL 29 (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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27A VAL* 4.4 10.3 - - + -
28A GLY* 1.3 77.6 - - - +
30A LYS* 1.3 57.1 + - - +
31A LEU* 4.1 2.4 + - + -
36A THR 3.8 0.5 - - - +
37A GLU* 2.7 13.1 - - - -
38A TYR* 2.5 58.8 + - + +
51A LEU* 4.2 22.2 - - + -
53A LEU* 4.4 4.7 - - + -
73A ILE* 4.3 15.7 - - + -
78A VAL* 3.9 36.1 - - + -
80A TYR 4.2 2.2 - - - +
81A ILE* 4.4 13.7 - - + -
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Residues in contact with LYS 30 (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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28A GLY 3.7 0.6 + - - -
29A VAL* 1.3 73.8 - - - +
31A LEU* 1.3 70.7 + - - +
35A SER* 3.5 41.0 + - - +
36A THR 3.7 3.1 - - - +
37A GLU* 4.2 19.3 - - + +
78A VAL* 3.8 2.9 - - - +
79A LEU* 2.8 32.6 + - + +
80A TYR* 3.3 57.8 + - + +
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Residues in contact with LEU 31 (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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29A VAL* 5.1 2.0 - - + -
30A LYS* 1.3 92.5 - - - +
32A LYS* 1.3 68.4 + - - +
33A PHE* 4.0 25.7 - - + +
35A SER 5.4 1.0 + - - -
36A THR* 3.1 32.3 + - + +
38A TYR* 3.4 41.3 - - + +
73A ILE* 5.1 4.7 - - + -
77A ASN* 3.0 36.8 - - + +
78A VAL* 4.5 7.0 - - + +
79A LEU* 3.8 5.3 - - - +
79G LEU* 3.8 16.8 - - + -
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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