Contacts of the strand formed by residues 72 - 76 (chain Q) in PDB entry 5A0Q
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 72 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68Q LEU* 3.6 5.1 + - + -
69Q ASN* 3.0 58.3 + - - +
70Q GLU 3.6 0.8 - - - -
71Q ASP* 1.4 114.4 - - + +
73Q ALA* 1.4 61.3 + - - +
104Q PRO* 4.9 11.2 - - + +
105Q ILE* 3.0 27.6 - - - +
106Q PRO* 4.6 0.2 - - + -
107Q CYS* 3.6 32.5 - - + +
110Q LEU* 4.6 5.8 - - + -
137Q ILE 3.6 7.0 - - - -
138Q GLY* 3.9 0.9 - - - -
140Q ASP* 4.1 23.1 - - - -
141Q LYS* 5.3 1.8 - - + +
216Q LEU* 4.9 0.7 - - - -
225Q ILE* 3.3 6.0 - - - +
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Residues in contact with ALA 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Q ILE* 3.5 14.1 - - + -
66Q TYR 3.1 19.1 - - - +
68Q LEU* 4.0 10.2 - - - +
72Q MET* 1.4 75.9 - - - +
74Q CYS* 1.4 60.1 + - - +
136Q TYR* 3.5 4.2 - - - +
137Q ILE* 2.9 45.4 + - + +
225Q ILE* 3.9 19.7 - - + -
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Residues in contact with CYS 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Q LEU* 4.5 0.4 - - - -
64Q LYS 4.1 0.5 - - - +
65Q ILE* 3.0 20.8 - - - +
66Q TYR* 3.2 25.9 + - - -
68Q LEU* 3.4 36.3 - - + -
73Q ALA* 1.4 74.2 - - - +
75Q SER* 1.4 60.7 + - - +
76Q VAL* 4.1 6.8 + - + -
87Q THR* 4.2 9.6 - - - -
90Q LEU* 4.2 12.1 - - + -
134Q LEU* 5.0 3.6 - - + -
135Q LEU 3.2 13.2 - - - +
136Q TYR* 4.3 5.4 - - + -
137Q ILE* 5.0 0.4 - - - +
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Residues in contact with SER 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q CYS* 3.1 26.1 - - - -
45Q LEU* 3.4 34.3 - - - +
47Q ALA* 4.5 5.7 - - - +
64Q LYS* 4.9 2.3 - - - +
65Q ILE* 4.6 7.0 + - - +
74Q CYS* 1.4 71.1 - - - +
76Q VAL* 1.3 64.8 + - - +
77Q ALA* 4.0 1.1 + - - +
133Q SER 3.9 0.5 - - - +
134Q LEU* 3.2 10.2 - - - +
135Q LEU* 3.0 35.5 + - - +
137Q ILE 5.7 0.2 - - - +
164Q ILE* 5.8 1.2 - - - +
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Residues in contact with VAL 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Q LYS* 3.7 45.3 + - + +
66Q TYR* 3.9 21.8 - - + -
74Q CYS* 4.4 6.7 - - - -
75Q SER* 1.3 76.9 + - - +
77Q ALA* 1.3 59.6 + - - +
79Q ILE 4.1 1.5 - - - +
83Q ALA* 2.8 36.1 - - + +
86Q LEU* 4.8 0.2 - - + -
87Q THR* 4.1 8.7 - - - +
132Q VAL* 3.2 13.9 - - + -
134Q LEU* 3.1 26.9 - - + -
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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