Contacts of the strand formed by residues 52 - 58 (chain B) in PDB entry 5I75
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 TYR 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B TYR* 1.3 72.8 - - - +
53B MET* 1.3 59.7 + - - +
54B ASN* 3.4 3.6 + - - +
69B ASN* 3.6 23.1 - - + -
70B ILE 3.4 15.0 - - - -
71B ASN* 3.4 40.4 + - + -
72B PRO* 4.4 0.4 - - + -
76B GLY 4.4 1.7 + - - -
117B ARG* 3.7 4.0 - - - +
118B SER* 2.9 47.2 + - - +
119B PRO* 4.2 2.2 - - - +
120B VAL* 3.9 38.2 - - + +
123B TYR* 3.7 25.6 - + - +
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Residues in contact with MET 53 (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 LEU* 4.6 7.9 - - + -
41B CYS* 4.1 20.9 - - - -
43B ALA* 4.5 6.5 - - + -
46B TYR* 3.2 27.4 - - - +
48B PHE* 4.2 17.3 - - + -
51B TYR 3.6 4.3 + - - +
52B TYR* 1.3 73.7 - - - +
54B ASN* 1.3 72.7 + - - +
55B TRP* 4.5 5.1 - - - +
68B GLY 4.1 0.2 - - - +
69B ASN* 3.1 1.9 - - - -
70B ILE* 2.9 51.3 + - + +
72B PRO* 5.0 6.5 - - + -
89B LEU* 4.7 0.7 - - - +
91B VAL* 5.9 0.7 - - + -
98B ALA* 3.5 26.2 - - + -
116B THR 3.9 15.3 - - - +
117B ARG* 4.4 6.3 - - + -
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Residues in contact with ASN 54 (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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52B TYR 3.4 4.2 + - - -
53B MET* 1.3 80.2 - - - +
55B TRP* 1.3 69.5 + - - +
66B TRP* 2.9 24.1 + - + +
68B GLY 3.3 5.6 - - - +
69B ASN* 3.2 4.6 - - - +
115B CYS* 3.1 8.5 - - - +
116B THR* 2.9 48.7 + - + +
118B SER* 2.3 34.8 + - - -
123B TYR* 2.4 25.4 + - - -
125B PHE* 3.8 7.4 - - + -
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Residues in contact with TRP 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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25B GLN* 4.1 5.6 - - - -
39B ILE* 3.7 36.3 - - + -
40B SER 3.4 21.5 - - - -
41B CYS* 3.7 12.3 - - + -
53B MET* 4.5 4.1 - - - +
54B ASN* 1.3 83.0 + - - +
56B VAL* 1.3 58.7 + - - +
66B TRP* 4.1 0.9 - - - -
67B ILE* 2.8 40.4 + - + +
68B GLY 3.0 10.5 + - - +
70B ILE* 5.5 1.7 - - + +
89B LEU* 3.4 31.0 - - + +
98B ALA* 4.1 15.4 - - - +
99B TYR 4.1 6.0 + - - -
100B MET* 3.6 47.5 - - + +
113B TYR* 4.7 1.3 - - + -
114B TYR* 3.1 28.9 - - - -
115B CYS* 3.6 25.3 - - + +
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Residues in contact with VAL 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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55B TRP* 1.3 76.2 - - - +
57B LYS* 1.3 62.7 + - - +
58B GLN 3.9 0.5 + - - -
64B LEU* 3.8 20.4 - - + -
65B GLU 3.6 26.2 - - - +
66B TRP* 4.4 10.1 - - + +
67B ILE* 4.4 2.2 - - - -
113B TYR* 3.6 2.2 - - - -
114B TYR* 2.9 36.2 + - + +
116B THR* 3.8 15.5 - - + -
125B PHE* 4.0 14.6 - - + -
128B TRP* 3.5 37.0 - - + -
118C PHE* 4.5 1.8 - - + -
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Residues in contact with LYS 57 (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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56B VAL* 1.3 72.3 - - - +
58B GLN* 1.3 66.3 + - - +
59B SER* 3.8 19.2 + - - +
63B SER 3.9 0.7 - - - +
64B LEU 3.6 0.3 - - - -
65B GLU* 2.8 61.5 + - + +
67B ILE* 3.7 18.9 - - + +
83B PHE* 4.0 21.4 - - + -
108B GLU* 3.5 26.1 + - - +
109B ASP* 4.2 12.3 + - - -
111B ALA* 4.4 4.9 - - + -
112B VAL 4.1 0.2 - - - -
113B TYR* 3.5 34.3 + - + +
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Residues in contact with GLN 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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56B VAL 3.9 0.4 + - - -
57B LYS* 1.3 73.3 - - - +
59B SER* 1.3 70.4 + - - +
62B LYS 4.0 5.9 + - - +
63B SER 3.9 9.4 - - - +
64B LEU* 3.5 20.7 - - + +
111B ALA* 3.2 3.1 - - - +
112B VAL* 2.9 47.9 + - + +
114B TYR* 3.2 21.0 + - + -
58C GLN* 2.7 45.9 + - - +
107C TYR* 3.6 15.0 + - - -
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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