Contacts of the strand formed by residues 40 - 51 (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 ASN 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B GLY* 3.4 1.2 - - - -
36B LYS* 2.9 44.5 + - + +
37B ASP* 2.7 39.5 + - - +
39B ASN* 1.3 86.1 + - - +
41B LEU* 1.3 59.7 + - - +
63B LYS 3.2 5.6 - - - -
64B ASP* 3.4 11.1 - - - +
65B GLY* 3.1 26.0 + - - +
112B LEU* 3.7 11.5 - - + +
114B LEU* 5.3 1.1 - - + -
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Residues in contact with LEU 41 (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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33B ASN* 3.6 44.0 - - + +
34B LEU 3.2 13.9 - - - +
37B ASP 3.2 22.2 - - - +
38B SER* 3.9 10.3 - - - +
40B ASN* 1.3 72.1 - - - +
42B CYS* 1.3 59.6 + - - +
43B LEU 3.2 10.3 - - - +
44B HIS* 4.7 2.2 - - + +
62B SER* 3.4 6.6 - - - -
63B LYS* 2.7 63.2 + - + +
68B TRP* 4.3 13.0 - - + -
112B LEU* 3.6 3.9 - - - +
119B TYR* 4.0 14.1 - - + -
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Residues in contact with CYS 42 (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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34B LEU 2.9 15.7 + - - -
35B GLY* 3.8 12.8 - - - -
40B ASN 3.9 1.2 + - - -
41B LEU* 1.3 73.2 - - - +
43B LEU* 1.3 64.6 + - - +
61B ASN 4.6 2.2 - - - -
62B SER* 4.7 1.2 - - - -
91B PHE* 6.1 1.3 - - - -
96B LEU* 3.8 37.0 - - + +
108B PHE* 3.7 21.3 - - - -
109B PRO 4.6 1.2 - - - +
110B ASN* 4.5 5.6 - - - +
111B ARG 5.4 1.9 + - - +
112B LEU* 3.6 30.2 - - + +
114B LEU* 4.7 9.0 - - + -
117B ILE* 4.3 15.7 - - - -
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Residues in contact with LEU 43 (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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32B LEU 3.5 1.5 - - - +
33B ASN* 3.4 4.5 - - - +
34B LEU* 2.8 62.3 + - + +
41B LEU* 3.2 4.2 - - - +
42B CYS* 1.3 81.8 - - - +
44B HIS* 1.3 69.3 + - - +
45B PHE* 4.3 20.6 - - + +
60B CYS* 4.7 7.0 - - + -
61B ASN 3.9 2.0 - - - -
89B ILE* 4.0 8.5 - - + -
96B LEU* 4.1 16.6 - - + -
98B VAL* 3.7 27.8 - - + -
108B PHE* 4.3 27.1 - - + -
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Residues in contact with HIS 44 (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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31B VAL* 3.8 26.5 - - + -
33B ASN* 2.6 28.5 + - - +
41B LEU* 4.7 4.9 - - + -
43B LEU* 1.3 72.5 - - - +
45B PHE* 1.3 56.7 + - - +
46B ASN* 3.3 15.2 - - + +
59B VAL* 3.3 5.0 - - + +
60B CYS* 3.2 9.5 - - - -
61B ASN* 2.8 40.2 + - + +
68B TRP* 3.5 29.2 - + + -
2C SGA 2.8 52.0 + - - -
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Residues in contact with PHE 45 (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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30B PHE* 4.9 3.4 - + - -
31B VAL* 3.2 2.8 - - - -
32B LEU* 2.8 62.8 + - + +
43B LEU* 3.7 13.9 - - + -
44B HIS* 1.3 70.9 - - - +
46B ASN* 1.3 57.9 + - - +
47B PRO* 3.4 26.2 - - + +
58B ILE* 3.7 22.7 - - + -
59B VAL 4.3 0.7 - - - -
60B CYS* 3.9 18.4 - - - -
79B PHE* 3.8 28.5 - + - -
87B VAL* 5.0 7.0 - - + -
89B ILE* 6.4 1.1 - - + -
98B VAL* 3.9 39.7 - - + -
106B PHE* 4.3 12.6 - + + -
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Residues in contact with ASN 46 (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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29B SER* 2.7 27.8 + - - -
30B PHE 2.8 21.8 + - - -
31B VAL* 3.4 13.4 - - + +
44B HIS* 3.3 23.8 - - + +
45B PHE* 1.3 74.6 - - - +
47B PRO* 1.3 61.8 + - - +
48B ARG* 2.7 39.1 + - - +
52B HIS* 4.9 2.4 - - - -
58B ILE* 4.5 0.4 - - - -
59B VAL* 3.0 36.7 + - + +
2C SGA 3.6 4.2 + - - +
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Residues in contact with PRO 47 (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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29B SER* 3.5 3.3 - - - -
30B PHE* 3.2 63.8 + - + +
45B PHE* 3.4 34.5 - - + +
46B ASN* 1.3 87.2 + - - +
48B ARG* 1.3 59.9 + - - +
49B PHE* 3.9 3.4 + - + -
57B THR 3.8 5.6 - - - +
58B ILE* 4.1 6.5 - - + -
77B PHE* 3.6 20.6 - - + -
79B PHE* 3.8 12.1 - - + -
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Residues in contact with ARG 48 (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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28B LYS 3.7 4.3 - - - +
29B SER* 4.2 6.7 - - - +
46B ASN* 2.7 29.7 + - - +
47B PRO* 1.3 71.0 - - - +
49B PHE* 1.3 61.8 + - - +
51B ALA* 3.6 24.0 - - + +
52B HIS* 3.8 15.8 - - - +
54B ASP* 3.2 29.6 + - + +
55B ALA 3.7 1.0 - - - -
56B ASN 2.9 20.6 + - - -
57B THR 2.8 23.8 + - - +
59B VAL* 3.7 26.6 - - - +
71B GLU* 3.6 4.0 + - - -
73B ARG* 3.7 0.6 - - - +
77B PHE* 3.7 3.0 - - - -
1C MAG 2.7 23.2 + - - -
2C SGA 2.9 49.7 + - - -
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Residues in contact with PHE 49 (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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23B VAL* 3.7 18.8 - - + -
27B ALA* 3.5 30.1 - - + +
28B LYS 2.7 25.8 + - - +
29B SER* 4.0 2.2 - - - -
30B PHE* 3.8 33.2 - + - -
47B PRO 4.3 3.4 - - - -
48B ARG* 1.3 71.0 - - - +
50B ASN* 1.3 63.5 + - + +
55B ALA* 3.2 4.3 - - - +
56B ASN* 2.8 34.2 + - - +
77B PHE* 3.5 28.0 - + - -
79B PHE* 3.7 10.1 - - + -
80B GLN 4.5 0.2 - - - -
81B PRO* 3.7 34.5 - - + -
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Residues in contact with ASN 50 (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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28B LYS* 3.2 22.0 + - + +
49B PHE* 1.3 83.4 - - + +
51B ALA* 1.3 62.9 + - - +
53B GLY* 5.0 4.5 + - - -
54B ASP 3.1 17.1 + - - +
55B ALA* 4.3 8.2 - - + +
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Residues in contact with ALA 51 (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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28B LYS* 4.2 9.6 + - + +
29B SER* 3.8 25.8 - - - -
48B ARG* 3.6 8.6 - - + +
50B ASN* 1.3 76.6 + - - +
52B HIS* 1.3 89.7 + - + +
53B GLY 3.1 3.1 - - - +
54B ASP* 3.0 22.0 + - - +
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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