Contacts of the strand formed by residues 41 - 48 (chain A) in PDB entry 1NS3
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 GLN 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A SER* 3.2 5.9 + - - -
38A THR* 2.8 39.8 + - + +
39A ALA 3.7 1.8 - - - -
40A THR* 1.3 86.6 + - - +
42A SER* 1.3 68.5 + - - +
43A PHE* 3.3 31.2 - - + +
55A VAL* 5.8 0.2 - - - +
57A HIS* 3.5 27.1 + - - +
58A GLY* 3.6 13.6 + - - -
40B THR 5.3 6.3 + - - -
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Residues in contact with SER 42 (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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35A VAL* 3.8 2.3 - - - +
36A VAL 2.8 19.4 + - - -
41A GLN* 1.3 80.9 - - - +
43A PHE* 1.3 63.6 + - - +
109A ARG* 2.6 44.2 + - - -
137A GLY* 3.5 9.9 - - - -
40B THR* 3.2 34.3 + - - +
41B GLN* 5.9 1.1 - - - -
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Residues in contact with PHE 43 (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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35A VAL* 3.6 6.9 - - - +
36A VAL* 3.0 51.6 + - + +
38A THR* 3.8 26.0 - - + -
41A GLN* 3.3 33.4 - - + +
42A SER* 1.3 77.4 + - - +
44A LEU* 1.3 67.2 + - - +
54A THR* 3.4 25.8 - - + -
55A VAL* 5.0 3.8 - - + -
58A GLY* 3.4 32.1 - - - -
59A ALA* 3.5 13.2 - - + -
109A ARG* 4.9 0.4 - - - -
137A GLY* 3.5 15.9 - - - +
139A SER* 3.5 16.6 - - - +
223C VAL* 4.5 2.2 - - + -
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Residues in contact with LEU 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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33A VAL* 4.4 9.6 - - + -
34A GLN 3.5 8.5 - - - +
35A VAL* 3.7 27.6 - - + -
36A VAL* 4.7 0.9 - - - -
43A PHE* 1.3 83.6 - - - +
45A ALA* 1.3 61.4 + - - +
54A THR* 2.8 20.4 + - - -
107A VAL 4.0 10.3 - - - +
108A THR 4.3 0.4 - - - +
109A ARG* 3.9 35.2 - - + +
137A GLY 4.1 7.6 - - - +
138A SER* 3.5 18.8 - - - +
139A SER 3.2 12.0 + - - +
140A GLY* 3.6 5.3 - - - -
141A GLY* 3.6 25.4 - - - +
229C ILE* 4.2 10.3 - - + -
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Residues in contact with ALA 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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32A GLU 4.3 0.2 - - - +
33A VAL* 3.4 1.9 - - - -
34A GLN* 2.8 34.4 + - + +
36A VAL* 4.0 23.1 - - + -
44A LEU* 1.3 77.7 - - - +
46A THR* 1.3 62.8 + - - +
52A CYS* 5.0 13.0 - - - -
53A TRP 3.2 16.6 - - - +
54A THR* 3.8 11.4 - - - +
85A TRP* 5.1 5.4 - - + -
140A GLY 4.4 0.4 - - - -
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Residues in contact with THR 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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32A GLU 3.6 5.8 - - - -
33A VAL* 4.0 12.3 - - + -
45A ALA* 1.3 78.1 - - - +
47A CYS* 1.3 63.1 + - - +
48A VAL* 3.7 13.3 + - - +
51A VAL 3.7 0.5 - - - +
52A CYS* 4.4 0.2 - - - -
53A TRP* 2.8 32.5 + - - +
94A LEU* 4.0 10.4 - - - +
140A GLY 2.9 27.1 - - - +
141A GLY* 3.8 2.0 - - - -
142A PRO* 3.6 28.2 - - + +
153A ILE* 3.6 15.5 - - + +
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Residues in contact with CYS 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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32A GLU 3.1 16.5 + - - +
34A GLN* 5.4 5.2 - - - -
46A THR* 1.3 70.5 - - - +
48A VAL* 1.3 61.7 + - - +
51A VAL 3.6 7.9 - - - +
52A CYS* 3.2 38.8 - - - -
87A ALA* 4.5 2.7 - - + -
91A ALA* 3.8 23.8 - - - -
92A ARG 3.5 11.1 - - - +
93A SER* 3.1 19.4 - - - +
94A LEU* 2.9 28.6 + - - +
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Residues in contact with VAL 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 THR* 3.7 17.4 + - - +
47A CYS* 1.3 75.7 - - - +
49A ASN* 1.3 85.6 + - - +
50A GLY 3.3 1.6 - - - -
51A VAL* 3.1 26.7 + - - +
53A TRP* 3.4 19.2 + - + +
94A LEU* 3.7 13.7 - - + +
96A PRO* 4.3 5.6 - - + -
150A ALA* 4.0 23.1 - - + -
153A ILE* 4.8 2.5 - - + -
172A VAL* 4.0 21.1 - - + -
175A MET* 4.4 13.7 - - + -
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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