Contacts of the strand formed by residues 43 - 51 (chain A) in PDB entry 2NSQ
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 PRO 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.9 20.9 - - + -
41A SER* 3.5 13.9 - - - +
42A ASP* 1.3 87.8 - - - +
44A TYR* 1.3 60.0 + - - +
65A THR* 3.4 0.8 - - - -
66A ILE* 2.9 42.3 + - - +
69A THR* 3.4 24.9 - - + +
72A PRO* 4.0 9.4 - - + -
74A TRP* 3.2 22.6 + - + -
93A VAL* 4.4 4.3 - - + -
94A PHE 3.1 10.3 - - - +
95A ASP* 4.4 0.2 - - - -
105A LEU* 4.8 2.9 - - + -
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Residues in contact with TYR 44 (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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43A PRO* 1.3 72.5 - - - +
45A VAL* 1.3 71.6 + - - +
46A LYS* 4.2 8.0 - - + +
62A GLN* 3.5 38.5 + - + -
63A THR* 3.4 14.1 - - - +
64A LYS 3.4 15.9 - - - +
65A THR* 3.6 17.7 - - - +
74A TRP* 3.7 4.3 - - - +
93A VAL* 3.4 5.5 - - - +
94A PHE* 2.9 69.5 + + + +
96A GLU* 3.7 19.7 - - + -
102A ASP* 2.6 36.4 + - - +
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Residues in contact with VAL 45 (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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26A VAL* 3.8 11.9 - - + -
44A TYR* 1.3 77.0 - - - +
46A LYS* 1.3 68.6 + - - +
47A LEU* 3.6 14.8 - - + +
62A GLN* 3.1 3.8 - - - +
63A THR* 2.8 46.6 + - + -
74A TRP* 3.4 38.1 - - + -
91A PHE* 4.1 24.0 - - + -
92A GLU 3.3 10.8 - - - +
93A VAL* 4.3 4.5 - - + -
146A LEU* 4.0 11.0 - - + -
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Residues in contact with LYS 46 (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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44A TYR* 4.0 10.6 - - + +
45A VAL* 1.3 72.2 - - - +
47A LEU* 1.3 63.3 + - - +
48A SER* 3.9 19.4 + - - +
57A GLU* 4.6 7.5 + - - -
60A LEU* 4.4 26.4 - - - +
61A VAL 3.6 9.0 - - - +
62A GLN* 4.0 10.5 - - + +
90A LEU 3.5 1.6 - - - +
91A PHE* 3.5 2.4 - - - -
92A GLU* 2.8 56.2 + - - +
94A PHE* 4.1 21.9 - - + -
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Residues in contact with LEU 47 (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 VAL* 4.2 2.5 - - + -
26A VAL* 3.9 11.0 - - + -
45A VAL* 3.6 27.8 - - + +
46A LYS* 1.3 74.2 - - - +
48A SER* 1.3 60.6 + - - +
49A LEU 4.2 0.7 - - - -
59A ALA 3.7 1.2 - - - +
60A LEU* 3.4 4.9 - - - +
61A VAL* 2.7 41.0 + - + +
63A THR* 4.3 7.0 - - + -
78A PHE* 3.9 25.8 - - + -
80A PHE* 3.8 36.2 - - + -
89A LEU* 4.6 4.0 - - + -
90A LEU 3.4 5.6 - - - +
91A PHE* 3.7 32.1 - - + -
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Residues in contact with SER 48 (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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46A LYS* 3.9 17.0 + - - +
47A LEU* 1.3 72.3 - - - +
49A LEU* 1.3 64.6 + - - +
50A TYR* 3.7 7.9 - - - -
57A GLU* 4.8 6.8 + - - -
59A ALA 3.4 4.3 - - - -
60A LEU* 3.4 22.5 - - - +
89A LEU* 3.5 4.4 - - - +
90A LEU* 2.8 52.0 + - - +
92A GLU* 4.4 6.8 + - - -
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Residues in contact with LEU 49 (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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10A TYR 4.6 2.5 - - - +
11A GLY* 4.7 2.5 - - - -
47A LEU 4.2 0.4 - - - -
48A SER* 1.3 73.0 - - - +
50A TYR* 1.3 56.8 + - - +
57A GLU* 3.6 2.9 - - - +
58A LEU* 2.7 53.9 + - + -
59A ALA* 2.9 26.5 + - + +
80A PHE* 4.1 15.6 - - + -
81A ARG 3.4 25.1 - - - +
82A VAL* 3.6 23.8 - - + -
87A HIS* 4.1 14.1 - - + +
88A ARG 3.6 13.7 - - - +
89A LEU* 3.6 18.6 - - + +
112A LEU* 4.1 6.1 - - + -
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Residues in contact with TYR 50 (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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48A SER* 3.7 15.0 - - - +
49A LEU* 1.3 77.9 - - - +
51A VAL* 1.3 81.7 + - - +
52A ALA* 4.3 1.3 - - - -
55A ASN* 3.1 32.7 + - + -
56A ARG 3.3 18.6 - - - +
57A GLU* 4.0 6.1 - - + +
58A LEU* 4.0 6.7 - - - +
87A HIS* 3.3 4.0 - - - +
88A ARG* 2.9 75.7 + - + +
90A LEU* 4.0 16.8 - - + -
109A ASP* 2.6 39.4 + - - -
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Residues in contact with VAL 51 (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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14A GLU* 4.8 0.4 - - - +
50A TYR* 1.3 78.6 - - - +
52A ALA* 1.3 70.0 + - - +
54A GLU* 3.6 28.5 - - + +
55A ASN 2.9 26.5 + - - -
56A ARG* 2.9 41.4 + - + +
58A LEU* 3.7 27.4 - - + -
86A ASN* 3.7 14.1 - - + +
87A HIS* 4.0 10.5 - - + +
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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