Contacts of the strand formed by residues 54 - 64 (chain A) in PDB entry 4Y1V
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 ASP 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ARG* 3.2 28.6 + - + +
49A PHE 3.8 0.5 - - - +
50A ASN* 3.5 6.3 + - - -
51A ALA 2.7 33.1 + - - +
52A HIS 3.5 9.5 - - - +
53A GLY* 1.3 84.3 - - - +
55A ALA* 1.3 61.1 + - - +
57A THR* 4.5 8.4 + - - +
73A ARG* 2.7 48.3 + - - +
1C MAG 4.7 1.7 - - - -
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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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49A PHE 3.2 10.1 - - - +
50A ASN* 5.1 7.4 - - - +
53A GLY 4.1 1.5 + - - +
54A ASP* 1.3 76.5 - - - +
56A ASN* 1.3 76.4 + - - +
57A THR* 2.9 14.5 + - - -
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Residues in contact with ASN 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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48A ARG 2.9 12.6 + - - -
49A PHE* 3.1 20.7 + - - +
55A ALA* 1.3 77.6 - - - +
57A THR* 1.3 57.7 + - - +
75A ALA 4.4 6.9 - - - +
77A PHE* 3.3 53.5 - - + +
79A PHE 5.0 1.2 + - - -
81A PRO* 5.9 2.0 - - - +
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Residues in contact with THR 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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48A ARG* 2.9 34.3 + - - +
54A ASP* 4.5 10.3 + - - +
55A ALA 2.9 22.7 + - - -
56A ASN* 1.3 74.8 + - - +
58A ILE* 1.3 65.8 + - - +
59A VAL* 3.6 2.7 + - + +
73A ARG* 3.8 44.8 + - + +
74A GLU 4.0 11.7 - - - +
75A ALA* 6.0 0.4 - - - -
77A PHE* 3.4 5.5 - - - -
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Residues in contact with ILE 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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45A PHE* 3.4 32.8 - - + -
46A ASN 3.9 2.5 - - - -
47A PRO* 4.2 7.6 - - + -
57A THR* 1.3 73.8 - - - +
59A VAL* 1.3 62.8 + - - +
60A CSO 3.7 17.1 + - - +
72A GLN 3.9 0.2 - - - +
73A ARG* 3.2 7.4 - - - +
74A GLU* 3.0 37.1 + - + -
76A VAL* 3.8 16.6 - - + +
77A PHE* 3.7 19.9 - - + -
78A PRO* 4.3 1.6 - - + -
79A PHE* 3.8 26.9 - - + -
100A LEU* 4.2 16.8 - - + -
106A PHE* 4.4 5.4 - - + -
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Residues in contact with VAL 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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44A HIS* 3.3 3.0 - - + +
46A ASN* 2.9 47.1 + - + +
48A ARG* 3.8 44.2 - - - +
57A THR* 4.3 5.2 - - + +
58A ILE* 1.3 75.4 - - - +
60A CSO 1.3 66.5 + - - +
71A GLU* 3.6 33.9 - - + +
72A GLN 3.7 2.9 - - - +
73A ARG* 3.8 24.2 - - + +
2C GAL 4.3 8.7 - - - +
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Residues in contact with CSO 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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43A LEU* 4.2 8.7 - - + -
44A HIS 3.2 5.8 - - - +
45A PHE* 3.9 25.4 - - - -
58A ILE* 3.7 13.8 - - - +
59A VAL* 1.3 78.6 - - - -
61A ASN* 1.3 62.4 + - - +
71A GLU* 3.6 2.4 - - - +
72A GLN* 2.7 48.9 + - - +
73A ARG 5.1 0.2 - - - -
74A GLU* 4.4 12.3 + - - +
106A PHE* 3.7 24.8 - - - -
108A PHE* 3.7 25.7 - - + -
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Residues in contact with ASN 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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43A LEU* 3.6 4.0 - - - -
44A HIS* 2.7 36.1 + - + -
60A CSO 1.3 76.8 - - - +
62A SER* 1.3 77.1 + - - +
68A TRP* 3.8 15.9 - - + +
69A GLY 3.0 41.8 + - - +
70A THR 3.2 5.9 - - - +
71A GLU* 3.7 14.3 - - - +
108A PHE* 3.6 13.4 - - - -
111A ARG* 3.3 0.9 + - - -
2C GAL 3.1 35.1 + - - +
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Residues in contact with SER 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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41A LEU* 3.3 13.7 - - - -
42A CSO 4.5 3.1 - - - -
44A HIS 4.8 0.4 - - - +
61A ASN* 1.3 83.9 + - - +
63A LYS* 1.3 60.7 + - - +
64A ASP* 5.4 2.1 + - - +
68A TRP* 3.3 14.5 - - - -
69A GLY* 2.9 28.2 + - - -
108A PHE* 4.5 6.1 - - - -
111A ARG* 3.0 40.0 + - - +
112A LEU* 4.2 12.4 - - - +
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Residues in contact with LYS 63 (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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38A SER 3.4 26.1 + - - +
39A ASN* 3.6 17.4 + - - +
40A ASN* 3.2 4.7 - - - -
41A LEU* 2.7 59.6 + - + +
62A SER* 1.3 75.0 - - - +
64A ASP* 1.3 61.2 + - - +
66A GLY* 3.8 26.8 + - - +
67A ALA 3.3 5.8 - - - +
68A TRP* 3.7 39.1 - - + +
112A LEU* 3.6 4.3 - - - +
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Residues in contact with ASP 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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40A ASN* 3.8 7.5 - - - +
62A SER* 4.3 2.2 - - - +
63A LYS* 1.3 74.3 - - - +
65A GLY* 1.3 69.6 + - - +
67A ALA* 2.8 28.4 + - + +
69A GLY 5.4 0.2 - - - +
111A ARG* 4.8 5.9 - - - +
112A LEU* 4.2 23.4 - - + +
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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