Contacts of the strand formed by residues 53 - 64 (chain A) in PDB entry 4PSQ
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 MET 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PHE* 4.1 22.0 - - + -
17A LYS* 4.1 33.4 - - + +
20A PHE* 4.7 2.0 - - + -
45A PHE* 4.1 21.5 - - + -
46A SER 3.4 15.3 - - - +
47A VAL* 4.3 3.4 - - + +
51A GLY 3.5 3.8 + - - -
52A GLN* 1.3 80.1 + - - +
54A SER* 1.3 67.6 + - - +
77A PHE* 3.1 59.0 + - + +
79A ASP* 5.3 1.6 + - - +
86A PHE* 3.8 34.3 - - + -
104A HIS* 5.2 2.7 - - + -
106A ILE* 5.5 1.1 - - + -
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Residues in contact with SER 54 (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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45A PHE* 3.6 1.7 - - - +
46A SER* 2.9 44.1 + - - +
47A VAL* 5.4 0.2 - - - -
48A ASP* 5.7 0.7 + - - +
52A GLN* 4.8 5.3 + - - -
53A MET* 1.3 79.7 - - - +
55A ALA* 1.3 65.4 + - - +
74A VAL* 6.1 1.3 - - - -
75A GLY 3.4 13.7 - - - -
76A THR* 4.3 11.9 - - - -
77A PHE* 3.7 6.1 - - - -
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Residues in contact with ALA 55 (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 GLU 3.3 13.2 - - - +
45A PHE* 3.8 23.8 - - + -
46A SER* 4.7 0.4 - - - +
54A SER* 1.3 76.8 + - - +
56A THR* 1.3 63.9 + - - +
74A VAL* 3.5 4.1 - - - +
75A GLY* 2.7 39.6 + - - +
77A PHE* 3.7 19.1 - - + -
201A 2WL 4.2 10.3 - - + -
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Residues in contact with THR 56 (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 ALA* 3.3 5.7 - - - +
44A GLU* 2.9 44.0 + - + +
55A ALA* 1.3 80.0 - - - +
57A ALA* 1.3 62.4 + - - +
73A MET 3.3 11.2 - - - +
74A VAL* 4.6 14.8 - - + -
201A 2WL 4.4 1.7 - - - -
214A EDO 2.7 23.5 + - - -
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Residues in contact with ALA 57 (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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37A LEU* 4.6 12.9 - - + +
41A ILE* 5.4 4.0 - - + -
42A VAL 3.4 8.1 - - - +
43A ALA* 4.8 5.8 - - + -
56A THR* 1.3 75.4 - - - +
58A LYS* 1.3 61.6 + - - +
71A ALA 3.5 2.9 - - - +
73A MET* 2.8 43.3 + - + +
201A 2WL 3.9 35.2 - - + -
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Residues in contact with LYS 58 (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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37A LEU* 4.7 2.5 - - - -
40A ASN 3.9 3.6 - - - +
41A ILE* 3.2 7.1 - - - +
42A VAL* 3.0 33.2 + - + +
56A THR* 6.1 0.2 - - - -
57A ALA* 1.3 75.6 - - - +
59A GLY* 1.3 58.9 + - - +
70A CYS* 5.5 1.6 - - - -
71A ALA 3.5 3.6 - - - -
72A ASP* 3.7 34.3 - - + +
174A CYS* 2.8 42.1 + - + +
175A ASP* 3.9 13.7 - - - +
214A EDO 3.5 39.0 + - - +
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Residues in contact with GLY 59 (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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37A LEU* 4.3 13.9 - - - +
39A ASP 3.5 10.5 - - - -
40A ASN 3.6 6.5 - - - -
41A ILE* 4.3 1.3 - - - -
58A LYS* 1.3 77.1 - - - +
60A ARG* 1.3 64.6 + - - -
70A CYS* 3.5 1.4 - - - -
71A ALA* 2.8 35.8 + - - +
174A CYS* 4.1 9.5 - - - -
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Residues in contact with ARG 60 (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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37A LEU* 3.8 0.9 - - - -
38A GLN* 2.8 55.7 + - - +
39A ASP* 2.5 62.2 + - - +
40A ASN* 4.9 0.7 - - + -
59A GLY* 1.3 73.5 - - - -
61A VAL* 1.3 56.0 + - - +
62A ARG* 4.2 17.2 - - - +
68A ASP* 2.7 33.7 + - + +
69A VAL 3.6 6.1 - - - +
173A TYR* 4.0 36.3 - - + -
174A CYS* 4.1 5.9 - - - -
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Residues in contact with VAL 61 (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 LEU* 4.0 31.2 - - + -
36A PHE 3.8 21.3 - - - +
37A LEU* 4.7 7.4 - - + -
38A GLN* 4.1 3.4 - - + -
60A ARG* 1.3 74.4 - - - +
62A ARG* 1.3 65.6 + - - +
63A LEU* 3.7 6.1 + - + -
68A ASP* 3.5 6.9 - - - +
69A VAL* 3.1 50.2 + - + +
71A ALA* 3.9 18.8 - - + -
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Residues in contact with ARG 62 (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 LEU* 3.8 20.5 - - + +
38A GLN* 3.8 15.1 - - + +
60A ARG* 4.2 14.8 - - - +
61A VAL* 1.3 75.9 - - - +
63A LEU* 1.3 79.5 + - - +
64A LEU* 3.3 23.8 + - - +
65A ASN* 2.9 29.1 + - - +
68A ASP* 3.4 15.9 + - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LEU* 5.2 9.2 - - + -
61A VAL* 4.4 9.9 - - + +
62A ARG* 1.3 92.8 + - - +
64A LEU* 1.3 73.9 + - + +
67A TRP* 3.0 45.7 + - + +
69A VAL* 3.9 40.2 - - + -
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Residues in contact with LEU 64 (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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62A ARG* 3.3 23.6 - - - +
63A LEU* 1.3 83.2 - - + +
65A ASN* 1.3 69.1 + - - +
66A ASN* 3.2 12.3 - - - +
67A TRP* 3.0 51.4 + - + +
68A ASP* 3.7 2.3 - - - +
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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