Contacts of the strand formed by residues 37 - 46 (chain Q) in PDB entry 4NYJ
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 GLU 37 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35Q THR* 4.0 0.4 - - - -
36Q ILE* 1.3 86.1 - - + +
38Q ASP* 1.3 68.3 + - - +
56Q LEU* 3.7 33.2 - - + +
57Q ASP 3.6 9.9 - - - +
58Q THR* 5.1 1.9 - - - +
70Q GLN* 3.2 25.5 + - - +
71Q TYR* 3.6 13.0 - - - +
619S ALA* 3.6 26.5 - - + +
621S PRO* 3.6 24.5 - - + +
691S ASN* 3.3 22.9 + - - +
695S HIS* 3.6 5.4 + - - -
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Residues in contact with ASP 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q SER* 4.7 0.9 + - - -
35Q THR* 3.7 16.9 + - - +
36Q ILE 5.5 0.2 + - - -
37Q GLU* 1.3 74.6 + - - +
39Q SER* 1.3 60.3 + - - +
40Q TYR* 3.8 31.7 + - + +
56Q LEU* 3.6 8.3 - - - +
57Q ASP* 2.9 43.5 + - + +
621S PRO* 4.8 0.7 - - - -
691S ASN* 4.6 0.5 - - - +
694S ARG* 3.5 24.3 + - - -
695S HIS* 3.1 30.2 + - - +
699S HIS* 5.9 1.3 + - - -
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Residues in contact with SER 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q ASP* 1.3 75.7 - - - +
40Q TYR* 1.3 77.7 + - - +
41Q ARG* 5.7 0.7 - - - +
54Q ASP* 4.1 13.3 + - - -
55Q ILE 3.5 7.4 + - - -
56Q LEU* 4.5 5.6 - - - +
621S PRO* 3.7 31.5 - - - +
622S ASN* 5.1 4.9 + - - +
695S HIS* 5.1 3.0 + - - -
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Residues in contact with TYR 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Q SER* 6.0 0.2 - - - -
20Q THR* 3.8 22.9 - - + -
21Q ILE* 4.1 28.9 - - + +
24Q ILE* 4.0 33.4 - - + -
25Q GLN* 5.1 10.8 - - - -
38Q ASP* 3.8 37.2 + - + +
39Q SER* 1.3 81.8 + - - +
41Q ARG* 1.3 69.1 + - - +
54Q ASP* 3.6 3.8 - - - +
55Q ILE* 2.8 41.0 + - + +
57Q ASP* 4.2 15.3 + - + -
699S HIS* 5.8 5.7 + + - -
976S ASN* 6.0 0.7 - - - -
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Residues in contact with ARG 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Q GLU* 3.8 11.5 + - - -
24Q ILE* 4.1 5.3 - - - +
39Q SER* 5.7 0.9 - - - +
40Q TYR* 1.3 79.2 - - - +
42Q LYS* 1.3 62.8 + - - +
52Q LEU* 3.5 31.7 - - + +
53Q LEU 3.2 5.8 - - - +
54Q ASP* 3.0 41.4 + - - +
55Q ILE* 6.0 0.2 - - - -
622S ASN* 4.7 17.0 + - - +
625S ARG* 6.1 2.0 - - - +
969S GLY* 5.4 9.4 - - - -
973S GLN* 3.6 26.3 - - + +
976S ASN* 4.0 15.0 + - - +
977S GLN* 5.6 0.2 + - - -
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Residues in contact with LYS 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q LEU* 3.6 45.8 + - + +
24Q ILE* 3.7 20.2 + - + -
26Q ASN* 5.8 0.4 + - - -
41Q ARG* 1.3 77.1 - - - +
43Q GLN* 1.3 71.0 + - - +
44Q VAL* 3.7 13.5 + - + +
51Q CYS 3.7 0.2 - - - +
52Q LEU* 4.0 3.1 - - - +
53Q LEU* 2.8 52.7 + - + +
55Q ILE* 5.1 0.2 - - + -
149Q ARG* 5.9 0.8 - - - +
157Q TYR* 3.7 22.7 - - - -
973S GLN* 4.0 2.7 - - - -
977S GLN* 4.2 25.7 - - - +
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Residues in contact with GLN 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Q MET* 3.7 23.7 - - + +
42Q LYS* 1.3 79.9 + - - +
44Q VAL* 1.3 63.7 + - - +
50Q THR* 4.2 3.8 - - + +
51Q CYS 3.6 3.6 - - - -
52Q LEU* 4.0 7.6 - - + +
919S LEU 3.1 20.9 + - - +
920S ARG* 3.7 13.2 + - - +
921S SER 4.1 0.4 - - - -
922S ILE* 2.7 31.8 + - - +
923S ASN* 4.6 0.2 - - - +
924S PRO* 3.3 21.5 - - + +
973S GLN* 3.0 26.4 + - - +
974S TYR* 2.7 29.7 + - - -
977S GLN* 4.3 1.9 + - - -
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Residues in contact with VAL 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Q LYS* 4.2 13.5 - - - +
43Q GLN* 1.3 80.0 - - - +
45Q VAL* 1.3 72.0 + - - +
46Q ILE* 3.7 23.6 - - + -
50Q THR* 3.7 1.2 - - - +
51Q CYS* 3.0 40.6 + - - +
53Q LEU* 4.0 19.5 - - + -
157Q TYR* 3.3 32.1 - - + +
923S ASN* 3.8 13.2 - - - +
924S PRO* 4.7 0.7 - - - -
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Residues in contact with VAL 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q VAL* 1.3 82.0 - - - +
46Q ILE* 1.3 63.4 + - - +
47Q ASP 4.3 0.2 + - - -
48Q GLY* 4.1 23.6 - - - +
49Q GLU 3.3 9.4 - - - +
50Q THR* 3.4 23.3 - - - +
157Q TYR* 5.6 2.1 - - - -
921S SER 3.8 10.1 - - - +
922S ILE 4.0 1.8 - - - +
923S ASN* 3.2 37.0 + - + +
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Residues in contact with ILE 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q VAL* 3.7 26.9 + - + -
45Q VAL* 1.3 77.6 - - - +
47Q ASP* 1.3 89.6 + - - +
48Q GLY 3.1 1.3 - - - -
49Q GLU* 2.9 24.9 + - - +
51Q CYS* 3.8 16.6 - - - -
53Q LEU* 4.7 0.4 - - + -
157Q TYR* 3.9 32.1 - - + +
160Q VAL* 3.8 25.8 - - + -
161Q ARG* 4.2 23.3 - - + +
164Q ARG* 4.5 6.3 + - - +
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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