Contacts of the strand formed by residues 54 - 64 (chain B) in PDB entry 4Y22
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ARG* 3.2 40.6 + - + +
50B ASN* 3.1 8.1 + - - +
51B ALA 3.0 31.7 + - - +
52B HIS 3.4 8.8 - - - +
53B GLY* 1.3 82.1 - - - +
55B ALA* 1.3 61.5 + - - +
56B ASN 4.2 0.2 - - - -
57B THR* 4.3 13.9 + - - +
59B VAL* 4.5 1.1 - - - -
73B ARG* 2.3 38.1 + - - -
1C MAG 3.6 2.1 + - - -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE 3.2 9.2 - - - +
50B ASN* 4.3 11.0 - - + +
53B GLY 4.2 1.6 + - - +
54B ASP* 1.3 73.6 - - - +
56B ASN* 1.3 75.3 + - + +
57B THR* 3.1 9.6 + - - -
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Residues in contact with ASN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ARG 2.9 8.0 + - - -
49B PHE* 2.8 28.1 + - - +
55B ALA* 1.3 77.7 - - - +
57B THR* 1.3 58.3 + - - +
75B ALA 4.9 5.4 - - - +
77B PHE* 3.3 48.3 - - + +
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Residues in contact with THR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ARG* 2.8 35.1 + - - +
54B ASP* 4.3 23.1 + - - +
55B ALA 3.1 19.2 + - - -
56B ASN* 1.3 74.4 + - - +
58B ILE* 1.3 73.4 + - - +
59B VAL* 3.6 2.3 + - + +
73B ARG* 4.3 20.0 - - + +
74B GLU 4.0 15.9 - - - +
75B ALA 5.9 0.4 - - - -
76B VAL 5.8 0.2 - - - -
77B PHE* 3.3 7.2 - - - -
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 3.7 26.9 - - + -
46B ASN 4.0 2.2 - - - -
47B PRO* 4.1 12.1 - - + -
57B THR* 1.3 72.3 - - - +
59B VAL* 1.3 63.2 + - - +
60B CYS* 3.9 14.2 + - - -
72B GLN 3.7 0.9 - - - +
73B ARG* 3.5 6.2 - - - -
74B GLU* 3.3 33.8 + - + +
76B VAL 3.8 13.8 + - - +
77B PHE* 3.7 20.1 - - + -
78B PRO* 4.0 4.0 - - + -
79B PHE* 3.8 19.7 - - + -
106B PHE* 3.5 36.8 - - + -
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS* 3.3 4.0 - - - +
46B ASN* 3.0 40.5 + - + +
48B ARG* 3.7 43.3 - - - +
54B ASP* 4.5 0.9 - - - -
57B THR* 4.3 6.7 - - + +
58B ILE* 1.3 75.0 - - - +
60B CYS* 1.3 63.8 + - - +
71B GLU* 3.8 37.7 - - + +
72B GLN 3.7 3.4 - - - +
73B ARG* 3.9 24.0 - - + +
2C SGA 4.8 5.2 - - - +
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Residues in contact with CYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.7 6.5 - - + -
44B HIS 3.2 7.0 - - - +
45B PHE* 3.9 20.9 - - - -
58B ILE* 3.9 21.3 - - - -
59B VAL* 1.3 76.6 - - - +
61B ASN* 1.3 62.6 + - - +
71B GLU* 3.4 1.9 - - - -
72B GLN* 2.6 46.0 + - + +
74B GLU* 4.9 10.3 - - - -
106B PHE* 5.7 5.2 - - - -
107B LYS 5.8 0.9 - - - -
108B PHE* 3.6 30.8 - - + -
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU 3.8 0.3 - - - -
44B HIS* 2.8 37.2 + - + -
59B VAL* 5.2 0.2 - - + -
60B CYS* 1.3 76.1 - - - +
62B SER* 1.3 80.4 + - - +
68B TRP* 3.7 20.0 - - + +
69B GLY* 3.0 38.5 + - - -
70B THR 3.4 0.6 + - - +
71B GLU* 3.3 17.7 - - + +
108B PHE* 3.5 17.8 - - - -
111B ARG* 3.4 4.2 + - - -
2C SGA 2.7 28.9 + - - +
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.4 12.6 - - - -
42B CYS 4.7 2.0 - - - -
44B HIS 5.0 0.4 - - - +
61B ASN* 1.3 84.5 + - - +
63B LYS* 1.3 61.0 + - - +
64B ASP* 5.9 0.7 - - - +
68B TRP* 3.2 14.9 - - - -
69B GLY* 2.8 27.0 + - - -
108B PHE* 4.0 7.0 - - - -
111B ARG* 3.1 40.2 + - - +
112B LEU* 4.2 11.8 - - - +
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER 3.4 24.7 + - - -
39B ASN* 3.3 18.7 + - - +
40B ASN* 3.2 4.5 - - - -
41B LEU* 2.7 58.1 + - + +
62B SER* 1.3 77.5 - - - +
64B ASP* 1.3 62.4 + - - +
66B GLY* 3.6 22.4 + - - +
67B ALA 3.3 19.3 - - - +
68B TRP* 3.6 35.7 - - + +
112B LEU* 3.5 5.7 - - - +
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Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASN* 3.4 11.0 - - - +
62B SER* 5.4 1.1 + - - +
63B LYS* 1.3 73.9 - - - +
65B GLY* 1.3 67.7 + - - +
66B GLY 3.2 0.6 + - - -
67B ALA* 3.1 23.6 + - - +
111B ARG 5.8 0.6 - - - +
112B LEU* 4.1 21.8 - - + +
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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